VCV000254248.2 - ClinVar

NM_013328.4(PYCR2):c.773T>C (p.Val258Ala)

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.

(2)

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.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_013328.4(PYCR2):c.773T>C (p.Val258Ala)

Variation ID: 254248 Accession: VCV000254248.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1q42.12 1: 225921232 (GRCh38) [ NCBI UCSC ] 1: 226108932 (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	Sep 18, 2016	Mar 23, 2024	Mar 20, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_013328.4:c.773T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_037460.2:p.Val258Ala	missense
NM_001271681.2:c.551T>C	NP_001258610.1:p.Val184Ala	missense
NC_000001.11:g.225921232A>G
NC_000001.10:g.226108932A>G
NG_044963.1:g.8109T>C

... more HGVS ... less HGVS

Protein change

V184A, V258A

Other names

Canonical SPDI

NC_000001.11:225921231:A:G

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

ClinGen: CA10586381 OMIM: 616406.0006 dbSNP: rs886037932 VarSome

Comment on variant

NCBI staff reviewed the paper by Zaki et al., 2016 (PubMed 27130255) to verify that the published locations for the coding position and the protein position were based on different reference sequences.

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.
PYCR2		-	-	GRCh38 GRCh37	122	160

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.
Hypomyelinating leukodystrophy 10	Likely pathogenic (2)	criteria provided, single submitter	Mar 20, 2024	RCV000240854.2

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.
Likely pathogenic (Mar 20, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Hypomyelinating leukodystrophy 10 (Autosomal recessive inheritance) Affected status: yes Allele origin: inherited	Centre for Inherited Metabolic Diseases, Karolinska University Hospital Accession: SCV004801681.1 First in ClinVar: Mar 23, 2024 Last updated: Mar 23, 2024	Zygosity: Homozygote
Pathogenic (Sep 16, 2016)	no assertion criteria provided Method: literature only	LEUKODYSTROPHY, HYPOMYELINATING, 10 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000299341.1 First in ClinVar: Sep 18, 2016 Last updated: Sep 18, 2016	Publications: PubMed (1) PubMed: 27130255 Comment on evidence: In 2 sibs, born of consanguineous Egyptian parents, with hypomyelinating leukodystrophy-10 (HLD10; 616420), Zaki et al. (2016) identified a homozygous c.773T-C transition in the PYCR2 … (more) In 2 sibs, born of consanguineous Egyptian parents, with hypomyelinating leukodystrophy-10 (HLD10; 616420), Zaki et al. (2016) identified a homozygous c.773T-C transition in the PYCR2 gene, resulting in a val184-to-ala (V184A) substitution at a highly conserved residue in the dimerization domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, and segregated with the disorder in the family. The variant was filtered against the ExAC database and an in-house exome database of 5,000 individuals. Functional studies of the variant and studies of patient cells were not performed. (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
PYCR2 Mutations cause a lethal syndrome of microcephaly and failure to thrive.	Zaki MS	Annals of neurology	2016	PMID: 27130255

Text-mined citations for rs886037932 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Mar 30, 2024

ClinVar Genomic variation as it relates to human health

NM_013328.4(PYCR2):c.773T>C (p.Val258Ala)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs886037932 ...