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NM_001365088.1(SLC12A6):c.1133G>T (p.Gly378Val) AND Agenesis of the corpus callosum with peripheral neuropathy

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 10, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004771404.1

Allele description [Variation Report for NM_001365088.1(SLC12A6):c.1133G>T (p.Gly378Val)]

NM_001365088.1(SLC12A6):c.1133G>T (p.Gly378Val)

Gene:
SLC12A6:solute carrier family 12 member 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q14
Genomic location:
Preferred name:
NM_001365088.1(SLC12A6):c.1133G>T (p.Gly378Val)
HGVS:
  • NC_000015.10:g.34252370C>A
  • NG_007951.1:g.90695G>T
  • NM_001042494.2:c.956G>T
  • NM_001042495.2:c.956G>T
  • NM_001042496.2:c.1106G>T
  • NM_001042497.2:c.1088G>T
  • NM_001365088.1:c.1133G>TMANE SELECT
  • NM_005135.2:c.980G>T
  • NM_133647.2:c.1133G>T
  • NP_001035959.1:p.Gly319Val
  • NP_001035960.1:p.Gly319Val
  • NP_001035961.1:p.Gly369Val
  • NP_001035962.1:p.Gly363Val
  • NP_001352017.1:p.Gly378Val
  • NP_005126.1:p.Gly327Val
  • NP_598408.1:p.Gly378Val
  • NP_598408.1:p.Gly378Val
  • LRG_270t1:c.980G>T
  • LRG_270t2:c.1133G>T
  • LRG_270:g.90695G>T
  • LRG_270p1:p.Gly327Val
  • LRG_270p2:p.Gly378Val
  • NC_000015.9:g.34544571C>A
  • NM_133647.1:c.1133G>T
Protein change:
G319V
Molecular consequence:
  • NM_001042494.2:c.956G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042495.2:c.956G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042496.2:c.1106G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042497.2:c.1088G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365088.1:c.1133G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005135.2:c.980G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_133647.2:c.1133G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Agenesis of the corpus callosum with peripheral neuropathy (ACCPN)
Synonyms:
Andermann syndrome; Charlevoix disease; Corpus callosum agenesis neuronopathy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0000902; MedGen: C0795950; Orphanet: 1496; OMIM: 218000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005375271NYU Undiagnosed Diseases Program, NYU School of Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Feb 10, 2024) 		germlineresearch

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedresearch

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From NYU Undiagnosed Diseases Program, NYU School of Medicine, SCV005375271.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedresearch PubMed (1)

Description

The glycine residue at this locus is conserved, and there are significant physiochemical differences between glycine and valine. Additionally, this variant is absent from the healthy population (gnomAD v4 database), and a functional assay demonstrates a detrimental effect on the encoded KCC3 protein function.

Description

The glycine residue at this locus is conserved, and there are significant physiochemical differences between glycine and valine. Additionally, this variant is absent from the healthy population (gnomAD v4 database), and a functional assay demonstrates a detrimental effect on the encoded KCC3 protein function. Note that this classification is based on unpublished functional assay results.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 3, 2024