VCV002435984.3 - ClinVar

NM_003038.5(SLC1A4):c.172_193del (p.Leu58fs)

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
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_003038.5(SLC1A4):c.172_193del (p.Leu58fs)

Variation ID: 2435984 Accession: VCV002435984.3

Type and length

Deletion, 22 bp

Location

Cytogenetic: 2p14 2: 64989807-64989828 (GRCh38) [ NCBI UCSC ] 2: 65216941-65216962 (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	Mar 5, 2023	Feb 20, 2024	Nov 20, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_003038.5:c.172_193del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_003029.2:p.Leu58fs	frameshift
NM_001193493.2:c.-134+1195_-134+1216del		intron variant
NM_001348406.2:c.-134+1195_-134+1216del		intron variant
NM_001348407.2:c.-134+1261_-134+1282del		intron variant
NC_000002.12:g.64989815_64989836del
NC_000002.11:g.65216949_65216970del
NG_053002.1:g.6371_6392del
NG_095373.1:g.515_536del

... more HGVS ... less HGVS

Protein change

L58fs

Other names

Canonical SPDI

NC_000002.12:64989806:GCGCGGGCCTGGGCGCGGCGTTGCGCGGGC:GCGCGGGC

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.
not provided	Pathogenic (1)	criteria provided, single submitter	Nov 20, 2023	RCV003679161.2
Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome	Uncertain significance (1)	criteria provided, single submitter	Mar 10, 2022	RCV003136734.3

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 (Mar 10, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV003823351.2 First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024
Pathogenic (Nov 20, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004403359.1 First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024	Publications: PubMed (3) PubMed: 26041762‚ 27848944‚ 30125339 Comment: This sequence change creates a premature translational stop signal (p.Leu58Serfs3) in the SLC1A4 gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Leu58Serfs3) in the SLC1A4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC1A4 are known to be pathogenic (PMID: 26041762, 27848944, 30125339). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC1A4-related conditions. ClinVar contains an entry for this variant (Variation ID: 2435984). For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This sequence change creates a premature translational stop signal (p.Leu58Serfs*3) in the SLC1A4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC1A4 are known to be pathogenic (PMID: 26041762, 27848944, 30125339). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC1A4-related conditions. ClinVar contains an entry for this variant (Variation ID: 2435984). For these reasons, this variant has been classified as Pathogenic.

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
Reanalysis of exome sequencing data of intellectual disability samples: Yields and benefits.	Al-Nabhani M	Clinical genetics	2018	PMID: 30125339
Clinical exome sequencing: results from 2819 samples reflecting 1000 families.	Trujillano D	European journal of human genetics : EJHG	2017	PMID: 27848944
Mutations in SLC1A4, encoding the brain serine transporter, are associated with developmental delay, microcephaly and hypomyelination.	Damseh N	Journal of medical genetics	2015	PMID: 26041762

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_003038.5(SLC1A4):c.172_193del (p.Leu58fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...