VCV001806468.1 - ClinVar

NM_024616.3(C3orf52):c.492T>A (p.Tyr164Ter)

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.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_024616.3(C3orf52):c.492T>A (p.Tyr164Ter)

Variation ID: 1806468 Accession: VCV001806468.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 3q13.2 3: 112112988 (GRCh38) [ NCBI UCSC ] 3: 111831835 (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	Dec 24, 2022	Dec 24, 2022	Dec 21, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_024616.3:c.492T>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_078892.3:p.Tyr164Ter	nonsense
NM_001171747.2:c.397-3654T>A		intron variant
NC_000003.12:g.112112988T>A
NC_000003.11:g.111831835T>A

Protein change

Y164*

Other names

C3ORF52, TYR164TER

Canonical SPDI

NC_000003.12:112112987:T:A

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

OMIM: 611956.0001 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.
C3orf52		-	-	GRCh38 GRCh38 GRCh37	11	41

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.
Hypotrichosis 15	Pathogenic (1)	no assertion criteria provided	Dec 21, 2022	RCV002472348.1

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.
Pathogenic (Dec 21, 2022)	no assertion criteria provided Method: literature only	HYPOTRICHOSIS 15 Affected status: not provided Allele origin: germline	OMIM Accession: SCV002769677.1 First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022	Publications: PubMed (1) PubMed: 32336749 Comment on evidence: In a brother and sister of Hispanic descent (family 1) with hypotrichosis (HYPT15; 620177), Malki et al. (2020) identified homozygosity for a c.492T-A transversion (c.492T-A, … (more) In a brother and sister of Hispanic descent (family 1) with hypotrichosis (HYPT15; 620177), Malki et al. (2020) identified homozygosity for a c.492T-A transversion (c.492T-A, NM_024616.2) in exon 5 of the C3ORF52 gene, resulting in a tyr164-to-ter (Y164X) substitution. The unaffected parents were heterozygous for the variant, which was present in heterozygous state in 1 of 119,840 individuals in the gnomAD database. C3ORF52 mRNA levels were markedly reduced in keratinocyte cultures from a skin biopsy from the affected sister, and immunostaining showed downregulation of C3ORF52 expression in a scalp skin sample from the same patient. Wildtype C3ORF52 was found to be expressed along the cell membrane, whereas the Y164X mutant colocalized with an endoplasmic reticulum marker, suggesting that the variant results not only in decreased C3ORF52 expression but also in protein mislocalization. Immunostaining of normal skin biopsies and coimmunoprecipitation assays in HeLa cells demonstrated colocalization of C3ORF52 and lipase H (LIPH; 607365), an association that was lost with the Y164X mutant. Analysis of HeLa cells cotransfected with LIPH and either wildtype or mutant C3ORF52 showed marked inhibition of LIPH-mediated lysophosphatidic acid biosynthesis with the mutant compared to wildtype C3ORF52. In addition, keratinocytes transfected with the Y164X variant showed a dramatic reduction in TGFA (190170) release levels compared to wildtype C3ORF52. (less)

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Loss-of-function variants in C3ORF52 result in localized autosomal recessive hypotrichosis.	Malki L	Genetics in medicine : official journal of the American College of Medical Genetics	2020	PMID: 32336749

Text-mined citations for this variant ...

Record last updated Jun 04, 2023

ClinVar Genomic variation as it relates to human health

NM_024616.3(C3orf52):c.492T>A (p.Tyr164Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...