VCV003236664.2 - ClinVar

NM_006295.3(VARS1):c.3203C>T (p.Thr1068Met)

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.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_006295.3(VARS1):c.3203C>T (p.Thr1068Met)

Variation ID: 3236664 Accession: VCV003236664.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 6p21.33 6: 31779693 (GRCh38) [ NCBI UCSC ] 6: 31747470 (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	May 27, 2024	Nov 30, 2024	May 20, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_006295.3:c.3203C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_006286.1:p.Thr1068Met	missense
NC_000006.12:g.31779693G>A
NC_000006.11:g.31747470G>A
NG_028229.1:g.21243C>T

Protein change

T1068M

Other names

NM_006295.3:c.3203C>T

Canonical SPDI

NC_000006.12:31779692:G: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

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.
VARS1		-	-	GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh37	179	217

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.
Neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy	Conflicting interpretations of pathogenicity (2)	criteria provided, conflicting classifications	May 20, 2024	RCV004556124.2

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.
Uncertain Significance (May 20, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: curation	Neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy (Autosomal recessive inheritance) Affected status: unknown Allele origin: germline	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard Accession: SCV005045242.1 First in ClinVar: May 26, 2024 Last updated: May 26, 2024	Other databases https://erepo.clinicalgenome.org… https://erepo.clinicalgenome.org/evrepo/ui/interpretation/d9e94c06-ca65-4169-8515-aff0aa2de957 Comment: The heterozygous p.Thr1068Met variant in VARS1 was identified by our study, in the compound heterozygous state, in trans with a VUS, in one individual with … (more) The heterozygous p.Thr1068Met variant in VARS1 was identified by our study, in the compound heterozygous state, in trans with a VUS, in one individual with neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy. The variant has been identified in 0.005% (3/62904) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP (rs777665186)). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. The number of missense variants reported in VARS1 in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, the clinical significance of the p.Thr1068Met variant is uncertain. ACMG/AMP Criteria applied: PM2_Supporting, PP2 (Richards 2015). (less)
Likely pathogenic (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy Affected status: yes Allele origin: germline	Juno Genomics, Hangzhou Juno Genomics, Inc Accession: SCV005416759.1 First in ClinVar: Nov 30, 2024 Last updated: Nov 30, 2024	Comment: PM2_Supporting+PM3_Supporting+ PP1+PP4+PM1

Comment:

The heterozygous p.Thr1068Met variant in VARS1 was identified by our study, in the compound heterozygous state, in trans with a VUS, in one individual with neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy. The variant has been identified in 0.005% (3/62904) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP (rs777665186)). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. The number of missense variants reported in VARS1 in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, the clinical significance of the p.Thr1068Met variant is uncertain. ACMG/AMP Criteria applied: PM2_Supporting, PP2 (Richards 2015).

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

Title	Author	Journal	Year	Link
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/d9e94c06-ca65-4169-8515-aff0aa2de957	-	-	-	-

Text-mined citations for this variant ...

Record last updated Dec 07, 2024

ClinVar Genomic variation as it relates to human health

NM_006295.3(VARS1):c.3203C>T (p.Thr1068Met)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...