VCV003027499.2 - ClinVar

NM_001178015.2(SLC4A10):c.417-1341del

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_001178015.2(SLC4A10):c.417-1341del

Variation ID: 3027499 Accession: VCV003027499.2

Type and length

Deletion, 1 bp

Location

Cytogenetic: 2q24.2 2: 161853628 (GRCh38) [ NCBI UCSC ] 2: 162710138 (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 11, 2024	Mar 16, 2024	Mar 8, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001178015.2:c.417-1341del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_001178016.2:c.450-1341del		intron variant
NM_001354440.2:c.417-1341del		intron variant
NM_001354441.2:c.450-1341del		intron variant
NM_001354442.2:c.450-1341del		intron variant
NM_001354443.2:c.453-1341del		intron variant
NM_001354444.2:c.417-1341del		intron variant
NM_001354445.2:c.450-1341del		intron variant
NM_001354446.2:c.417-1341del		intron variant
NM_001354447.2:c.453-1341del		intron variant
NM_001354448.2:c.450-1341del		intron variant
NM_001354449.2:c.417-1341del		intron variant
NM_001354450.2:c.417-1341del		intron variant
NM_001354451.2:c.417-1341del		intron variant
NM_001354453.2:c.270-1341del		intron variant
NM_001354455.2:c.-269-1341del		intron variant
NM_001354460.2:c.453-1341del		intron variant
NM_001354461.2:c.453-1341del		intron variant
NM_022058.4:c.417-1341del		intron variant
NC_000002.12:g.161853629del
NC_000002.11:g.162710139del
NG_021401.1:g.234295del

... more HGVS ... less HGVS

Protein change

Other names

EX5-11DEL

Canonical SPDI

NC_000002.12:161853627:AA: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: 605556.0001 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.
SLC4A10		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	101	127

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 hypotonia and characteristic brain abnormalities	Pathogenic (1)	no assertion criteria provided	Mar 8, 2024	RCV003889361.2

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 08, 2024)	no assertion criteria provided Method: literature only	NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA AND CHARACTERISTIC BRAIN ABNORMALITIES Affected status: not provided Allele origin: germline	OMIM Accession: SCV004704604.2 First in ClinVar: Mar 10, 2024 Last updated: Mar 16, 2024	Publications: PubMed (1) PubMed: 37459438 Comment on evidence: In 2 Palestinian sibs (family 1), born to consanguineous parents, with neurodevelopmental disorder with hypotonia and characteristic brain abnormalities (NEDHBA; 620746), Fasham et al. (2023) … (more) In 2 Palestinian sibs (family 1), born to consanguineous parents, with neurodevelopmental disorder with hypotonia and characteristic brain abnormalities (NEDHBA; 620746), Fasham et al. (2023) identified homozygosity for a deletion of exons 5-11 (c.417-1341del, NM_001178015.2) of the SLC4A10 gene, predicted to result in a frameshift and premature termination (Trp140ArgfsTer39). The mutation, which was identified by whole-genome sequencing, was not present in the gnomAD database (v2.1.1 and v3.1.1). (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
SLC4A10 mutation causes a neurological disorder associated with impaired GABAergic transmission.	Fasham J	Brain : a journal of neurology	2023	PMID: 37459438

Text-mined citations for this variant ...

Record last updated Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_001178015.2(SLC4A10):c.417-1341del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...