VCV002499988.2 - ClinVar

NM_003038.5(SLC1A4):c.2T>C (p.Met1Thr)

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_003038.5(SLC1A4):c.2T>C (p.Met1Thr)

Variation ID: 2499988 Accession: VCV002499988.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 2p14 2: 64989645 (GRCh38) [ NCBI UCSC ] 2: 65216779 (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	Apr 30, 2023	Sep 3, 2023	Mar 1, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_003038.5:c.2T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_003029.2:p.Met1Thr	missense initiator codon variant
NM_001193493.2:c.-134+1025T>C		intron variant
NM_001348406.2:c.-134+1025T>C		intron variant
NM_001348407.2:c.-134+1091T>C		intron variant
NC_000002.12:g.64989645T>C
NC_000002.11:g.65216779T>C
NG_053002.1:g.6201T>C
NG_095373.1:g.345T>C

... more HGVS ... less HGVS

Protein change

M1T

Other names

Canonical SPDI

NC_000002.12:64989644:T:C

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.
SLC1A4		-	-	GRCh38 GRCh37	388	407

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.
Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome	Pathogenic (1)	no assertion criteria provided	Mar 1, 2023	RCV003224078.2

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.
Pathogenic (Mar 01, 2023)	no assertion criteria provided Method: clinical testing	Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome Affected status: yes Allele origin: germline	Payam Genetics Center, General Welfare Department of North Khorasan Province Accession: SCV003919722.2 First in ClinVar: Apr 30, 2023 Last updated: Sep 03, 2023 Comment: (p.M1T)	Comment: The SLC1A4 c.2T>C(p.M1T) results is a missense mutation and results is loss of start codon, predicted lead to disease. This variant is not present in … (more) The SLC1A4 c.2T>C(p.M1T) results is a missense mutation and results is loss of start codon, predicted lead to disease. This variant is not present in population databases (ExAC no frequency) and was not found in 1000G, Genom AD exome, genome and Iranom. This variant has not been reported in the literature in individuals affected with SLC1A4-related conditions. We detected two brothers with similar clinical symptoms witch one of them died at 7 years old and one of them have been analyzed and detected homozygous c.2T>C variation at this SLC1A4 gene, the parents are consanguineous and both are carrier for this mutation. We classified this variant as Pathogenic according to our clinical evidence from this family. (less) Number of individuals with the variant: 3 Age: 0-9 years Sex: mixed Ethnicity/Population group: Iranian Geographic origin: Iran

Comment:

The SLC1A4 c.2T>C(p.M1T) results is a missense mutation and results is loss of start codon, predicted lead to disease. This variant is not present in population databases (ExAC no frequency) and was not found in 1000G, Genom AD exome, genome and Iranom. This variant has not been reported in the literature in individuals affected with SLC1A4-related conditions. We detected two brothers with similar clinical symptoms witch one of them died at 7 years old and one of them have been analyzed and detected homozygous c.2T>C variation at this SLC1A4 gene, the parents are consanguineous and both are carrier for this mutation. We classified this variant as Pathogenic according to our clinical evidence from this family.

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 May 08, 2024

ClinVar Genomic variation as it relates to human health

NM_003038.5(SLC1A4):c.2T>C (p.Met1Thr)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...