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NM_015378.4(VPS13D):c.5723T>C (p.Ile1908Thr) AND Neurodevelopmental disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 18, 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:
RCV003985139.1

Allele description [Variation Report for NM_015378.4(VPS13D):c.5723T>C (p.Ile1908Thr)]

NM_015378.4(VPS13D):c.5723T>C (p.Ile1908Thr)

Gene:
VPS13D:vacuolar protein sorting 13 homolog D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.22
Genomic location:
Preferred name:
NM_015378.4(VPS13D):c.5723T>C (p.Ile1908Thr)
HGVS:
  • NC_000001.11:g.12288311T>C
  • NG_056877.1:g.63273T>C
  • NM_015378.4:c.5723T>CMANE SELECT
  • NM_018156.4:c.5723T>C
  • NP_056193.2:p.Ile1908Thr
  • NP_060626.2:p.Ile1908Thr
  • LRG_1213t1:c.5723T>C
  • LRG_1213:g.63273T>C
  • LRG_1213p1:p.Ile1908Thr
  • NC_000001.10:g.12348368T>C
Protein change:
I1908T
Molecular consequence:
  • NM_015378.4:c.5723T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018156.4:c.5723T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Neurodevelopmental disorder
Identifiers:
MONDO: MONDO:0700092; MeSH: D065886; MedGen: C1535926

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004801426SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 18, 2024) 		unknowncuration

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders.

Sultan T, Scorrano G, Panciroli M, Christoforou M, Raza Alvi J, Di Ludovico A, Qureshi S, Efthymiou S, Salpietro V, Houlden H.

Gene. 2024 Mar 20;899:148119. doi: 10.1016/j.gene.2023.148119. Epub 2023 Dec 29.

PubMed [citation]
PMID:
38160741

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 SIB Swiss Institute of Bioinformatics, SCV004801426.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (2)

Description

This variant is interpreted for neurodevelopmental disorder, autosomal recessive. The following ACMG Tag(s) were applied: Cosegregation with disease in multiple affected family members (PP1). Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease (PP2).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 23, 2024