NM_003754.3(EIF3F):c.694T>G (p.Phe232Val) AND Intellectual developmental disorder, autosomal recessive 67
- Germline classification:
- Pathogenic/Likely pathogenic (17 submissions)
- Last evaluated:
- Dec 21, 2023
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000754608.29
Allele description [Variation Report for NM_003754.3(EIF3F):c.694T>G (p.Phe232Val)]
NM_003754.3(EIF3F):c.694T>G (p.Phe232Val)
- Gene:
- EIF3F:eukaryotic translation initiation factor 3 subunit F [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 11p15.4
- Genomic location:
- Preferred name:
- NM_003754.3(EIF3F):c.694T>G (p.Phe232Val)
- Other names:
- EIF3F, PHE232VAL (rs141976414)
- HGVS:
- NC_000011.10:g.7994466T>G
- NM_003754.3:c.694T>GMANE SELECT
- NP_003745.1:p.Phe232Val
- NC_000011.9:g.8016013T>G
- NM_003754.2:c.694T>G
This HGVS expression did not pass validation- Protein change:
- F232V; PHE232VAL
- Links:
- OMIM: 603914.0001; dbSNP: rs141976414
- NCBI 1000 Genomes Browser:
- rs141976414
- Molecular consequence:
- NM_003754.3:c.694T>G - missense variant - [Sequence Ontology: SO:0001583]
- Observations:
- 3
Condition(s)
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000882521 | OMIM | no assertion criteria provided | Pathogenic (Jul 21, 2022) | germline | literature only | |
SCV001194261 | SIB Swiss Institute of Bioinformatics | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Oct 18, 2019) | unknown | curation | |
SCV001370395 | Centre for Mendelian Genomics, University Medical Centre Ljubljana | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Oct 27, 2019) | unknown | clinical testing | |
SCV001429204 | Institute of Human Genetics, University of Leipzig Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 11, 2023) | unknown | clinical testing | |
SCV001521276 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | unknown | clinical testing | |
SCV001994799 | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 28, 2021) | unknown | clinical testing | |
SCV002029189 | Clinical Genetics Laboratory, University Hospital Schleswig-Holstein | no assertion criteria provided | Pathogenic (Oct 14, 2021) | germline | clinical testing | |
SCV002058452 | 3billion | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 3, 2022) | germline | clinical testing | PubMed (1) PMID:30409806, |
SCV002580498 | MGZ Medical Genetics Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Jul 4, 2022) | germline | clinical testing | |
SCV003844423 | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) | Pathogenic (Feb 7, 2023) | germline | clinical testing | |
SCV004013255 | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jun 1, 2023) | germline | clinical testing | |
SCV004045933 | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | criteria provided, single submitter (Classification criteria August 2017) | Pathogenic (Nov 7, 2022) | inherited | clinical testing | |
SCV004177071 | Clinical Genomics Laboratory, Washington University in St. Louis | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 2, 2023) | germline | clinical testing | |
SCV004238169 | Revvity Omics, Revvity | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Jun 2, 2023) | germline | clinical testing | |
SCV004814245 | North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Feb 11, 2021) | germline | clinical testing | |
SCV005038668 | Institute of Human Genetics, University Hospital of Duesseldorf | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | not provided | |
SCV005086688 | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
| criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Dec 21, 2023) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing, curation |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | yes | 2 | not provided | not provided | 1 | not provided | clinical testing, not provided |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | inherited | yes | 1 | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
Citations
PubMed
Quantifying the contribution of recessive coding variation to developmental disorders.
Martin HC, Jones WD, McIntyre R, Sanchez-Andrade G, Sanderson M, Stephenson JD, Jones CP, Handsaker J, Gallone G, Bruntraeger M, McRae JF, Prigmore E, Short P, Niemi M, Kaplanis J, Radford EJ, Akawi N, Balasubramanian M, Dean J, Horton R, Hulbert A, Johnson DS, et al.
Science. 2018 Dec 7;362(6419):1161-1164. doi: 10.1126/science.aar6731. Epub 2018 Nov 8.
- PMID:
- 30409806
- PMCID:
- PMC6726470
Hüffmeier U, Kraus C, Reuter MS, Uebe S, Abbott MA, Ahmed SA, Rawson KL, Barr E, Li H, Bruel AL, Faivre L, Tran Mau-Them F, Botti C, Brooks S, Burns K, Ward DI, Dutra-Clarke M, Martinez-Agosto JA, Lee H, Nelson SF; UCLA California Center for Rare Disease., Zacher P, et al.
Orphanet J Rare Dis. 2021 Mar 18;16(1):136. doi: 10.1186/s13023-021-01744-1.
- PMID:
- 33736665
- PMCID:
- PMC7977188
Details of each submission
From OMIM, SCV000882521.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (2) |
Description
In 9 patients from 7 unrelated European families with an intellectual development disorder (MRT67; 618295), Martin et al. (2018) found homozygosity for a c.694T-C transition in the EIF3F gene resulting in a phenylalanine-to-valine substitution in codon 232 (F232V). This variant, rs141976414, is present at a frequency of 0.12% among non-Finnish Europeans in gnomAD, but no homozygotes were reported. The phenylalanine at position 232 is evolutionarily conserved and was predicted to stabilize the protein. Western blots showed that EIF3F protein levels were 27% lower in homozygous cells relative to heterozygous and wildtype iPSCs. Translation rate and cell proliferation rate were reduced, but not viability.
In 21 newly reported patients from 16 families with MRT67, Huffmeier et al. (2021) identified a c.694T-C transition (c.694T-C, NM_003754) in the EIF3F gene, resulting in the F232V substitution. The mutation was found in homozygous state in 20 patients and in compound heterozygous state with a 1-bp duplication (c.861dup, 603914.0002) in 1 patient. Haplotype analysis showed that the F232V variant was on an identical haplotype in 15 affected individuals of all tested families, suggesting a founder effect. The patient (P3) with the c.861dup mutation had motor and speech development and postnatal growth on the severe end of the spectrum compared with patients homozygous for F232V. The c.861dup variant was not present in the gnomAD database.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From SIB Swiss Institute of Bioinformatics, SCV001194261.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | curation | PubMed (2) |
Description
This variant is interpreted as Likely pathogenic for Intellectual developmental disorder, autosomal recessive 67. The following ACMG Tag(s) were applied: PM2, PP3, PS3-Moderate, PM3.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001370395.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics, University of Leipzig Medical Center, SCV001429204.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant was identified as homozygous._x000D_ Criteria applied: PM3_VSTR, PS3, PM1_STR
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Baylor Genetics, SCV001521276.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV001994799.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Clinical Genetics Laboratory, University Hospital Schleswig-Holstein, SCV002029189.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From 3billion, SCV002058452.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
Description
Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000617475, PMID:30409806, PS1_S). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000711, PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.759, 3CNET: 0.883, PP3_P). A missense variant is a common mechanism associated with Mental retardation (PP2_P). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (PMID:30409806, PM3_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From MGZ Medical Genetics Center, SCV002580498.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003844423.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (2) |
Description
Variant summary: EIF3F c.694T>G (p.Phe232Val) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0007 in 251224 control chromosomes, predominantly at a frequency of 0.0012 within the Non-Finnish European subpopulation in the gnomAD database. c.694T>G has been reported in the literature in multiple homozygous individuals and at least one compound heterozygous individual affected with Autosomal Recessive Intellectual Developmental Disorder from at least 23 different families (e.g. Martin_2018, Huffmeier_2021). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and found that the variant results in reduced protein expression, approximately 70% of WT, and was associated with reduced protein translation and cellular proliferation rates (Martin_2018). Haplotype analyses have suggested that c.694T>G may be a common founder variant within populations of European ancestry (Huffmeier_2021). Fifteen submitters have provided clinical-significance assessments for this variant to ClinVar after 2014. The majority classified the variant as either pathogenic (n=10) or likely pathogenic (n=4), and one classified it as VUS. Based on the evidence outlined above, the variant was classified as pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV004013255.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
PS3, PM3_Strong, PP3
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV004045933.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Clinical Genomics Laboratory, Washington University in St. Louis, SCV004177071.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
The EIF3F c.694T>G (p.Phe232Val) variant has been published in the compound heterozygous or homozygous state in at least 21 individuals with intellectual disability ranging from mild to moderate, and approximately half of affected individuals also displayed behavioral problems, hearing loss, and short stature (Hüffmeier U et al., PMID: 33736665; Martin HC et al., PMID: 30409806). This variant has been reported in the ClinVar database as a germline pathogenic or likely pathogenic variant by 19 submitters. The highest population minor allele frequency in the population database genome aggregation database (v.2.1.1) is 0.12% in the European (non-Finnish) population and this variant has been implicated as a founder variant (Hüffmeier U et al., PMID: 33736665). Computational predictors indicate that the variant is damaging, evidence that correlates with impact to EIF3F3 function. In support of this prediction, functional studies show that this variant causes reduced global translation and impairs cellular proliferation (Martin HC et al., PMID: 30409806). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Revvity Omics, Revvity, SCV004238169.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, SCV004814245.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
Criteria Codes: PS3_Mod PP1_Str PP3
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics, University Hospital of Duesseldorf, SCV005038668.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | not provided | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005086688.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (2) |
Description
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Intellectual developmental disorder, autosomal recessive 67 (MIM#618295). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from phenylalanine to valine. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (201 heterozygotes, 0 homozygotes). (SP) 0309 - Multiple alternative amino acid changes at the same position have been observed in gnomAD (highest allele count (v3): 2 heterozygotes, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic or likely pathogenic by multiple clinical laboratories in ClinVar and has been observed in many homozygous and at least one compound heterozygous individual with a neurodevelopmental disorder (PMID: 33736665). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: Oct 8, 2024