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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 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no 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
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)

Name:
Intellectual developmental disorder, autosomal recessive 67
Synonyms:
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 67
Identifiers:
MONDO: MONDO:0032662; MedGen: C4749019; OMIM: 618295

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000882521OMIM
no assertion criteria provided
Pathogenic
(Jul 21, 2022)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV001194261SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 18, 2019)
unknowncuration

PubMed (2)
[See all records that cite these PMIDs]

SCV001370395Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 27, 2019)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001429204Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 11, 2023)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001521276Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001994799Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 28, 2021)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002029189Clinical Genetics Laboratory, University Hospital Schleswig-Holstein
no assertion criteria provided
Pathogenic
(Oct 14, 2021)
germlineclinical testing

SCV0020584523billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 3, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

PMID:30409806,

SCV002580498MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jul 4, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003844423Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Feb 7, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV004013255Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 1, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004045933Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
criteria provided, single submitter

(Classification criteria August 2017)
Pathogenic
(Nov 7, 2022)
inheritedclinical testing

Citation Link,

SCV004177071Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 2, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004238169Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jun 2, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004814245North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Feb 11, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005038668Institute of Human Genetics, University Hospital of Duesseldorf
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlinenot provided

PubMed (1)
[See all records that cite this PMID]

SCV005086688Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 21, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing, curation
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes2not providednot provided1not providedclinical testing, not provided
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedinheritedyes1not providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical 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.

PubMed [citation]
PMID:
30409806
PMCID:
PMC6726470

EIF3F-related neurodevelopmental disorder: refining the phenotypic and expanding the molecular spectrum.

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.

PubMed [citation]
PMID:
33736665
PMCID:
PMC7977188
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000882521.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From SIB Swiss Institute of Bioinformatics, SCV001194261.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001370395.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001429204.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was identified as homozygous._x000D_ Criteria applied: PM3_VSTR, PS3, PM1_STR

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001521276.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV001994799.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics Laboratory, University Hospital Schleswig-Holstein, SCV002029189.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002058452.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From MGZ Medical Genetics Center, SCV002580498.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003844423.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV004013255.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

PS3, PM3_Strong, PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV004045933.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided1not providednot providednot provided

From Clinical Genomics Laboratory, Washington University in St. Louis, SCV004177071.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV004238169.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, SCV004814245.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Criteria Codes: PS3_Mod PP1_Str PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University Hospital of Duesseldorf, SCV005038668.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot provided PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005086688.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024