VCV003256536.1 - ClinVar

NM_001242882.2(NAXD):c.269G>T (p.Cys90Phe)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001242882.2(NAXD):c.269G>T (p.Cys90Phe)

Variation ID: 3256536 Accession: VCV003256536.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 13q34 13: 110625215 (GRCh38) [ NCBI UCSC ] 13: 111277562 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Aug 4, 2024	Aug 4, 2024	Jul 30, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001242882.2:c.269G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001229811.1:p.Cys90Phe	missense
NM_001242881.2:c.323G>T	NP_001229810.1:p.Cys108Phe	missense
NM_001242883.2:c.57-2224G>T		intron variant
NM_018210.4:c.323G>T	NP_060680.2:p.Cys108Phe	missense
NR_040103.1:n.411G>T		non-coding transcript variant
NC_000013.11:g.110625215G>T
NC_000013.10:g.111277562G>T

... more HGVS ... less HGVS

Protein change

C108F, C90F

Other names

Canonical SPDI

NC_000013.11:110625214:G:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
NAXD		-	-	GRCh38 GRCh37	142	279

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
NAD(P)HX dehydratase deficiency	Uncertain significance (1)	criteria provided, single submitter	Jul 30, 2024	RCV004596007.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Jul 30, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NAD(P)HX dehydratase deficiency (Autosomal recessive inheritance) Affected status: yes Allele origin: maternal	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan Accession: SCV005088912.1 First in ClinVar: Aug 04, 2024 Last updated: Aug 04, 2024	Comment: The missense variant c.269G>T, p.(Cys90Phe) was identified in compound heterozygosity with the variant c.922C>T (Clinvar ID: 617755). This variant is found at an extremely low … (more) The missense variant c.269G>T, p.(Cys90Phe) was identified in compound heterozygosity with the variant c.922C>T (Clinvar ID: 617755). This variant is found at an extremely low frequency in the gnomAD population database (0.00000186), where homozygotes are not reported. It has not been previously reported in databases associated with pathologies or in the literature. In silico analysis using different predictive algorithms shows contradictory results regarding its pathogenicity. According to the ACMG criteria, the variant is classified as of uncertain significance. (less) Clinical Features: Progressive encephalopathy (present) , Seizure (present) , Chorea (present) , mucositis (present) , Sideroblastic anemia (present) , Bilateral basal ganglia lesions (present) , Developmental regression … (more) Progressive encephalopathy (present) , Seizure (present) , Chorea (present) , mucositis (present) , Sideroblastic anemia (present) , Bilateral basal ganglia lesions (present) , Developmental regression (present) (less) Sex: male

Comment:

The missense variant c.269G>T, p.(Cys90Phe) was identified in compound heterozygosity with the variant c.922C>T (Clinvar ID: 617755). This variant is found at an extremely low frequency in the gnomAD population database (0.00000186), where homozygotes are not reported. It has not been previously reported in databases associated with pathologies or in the literature. In silico analysis using different predictive algorithms shows contradictory results regarding its pathogenicity. According to the ACMG criteria, the variant is classified as of uncertain significance.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Aug 11, 2024

ClinVar Genomic variation as it relates to human health

NM_001242882.2(NAXD):c.269G>T (p.Cys90Phe)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...