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NM_015378.4(VPS13D):c.10818_10821del (p.Gly3607fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 19, 2023
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:
RCV003669414.1

Allele description [Variation Report for NM_015378.4(VPS13D):c.10818_10821del (p.Gly3607fs)]

NM_015378.4(VPS13D):c.10818_10821del (p.Gly3607fs)

Gene:
VPS13D:vacuolar protein sorting 13 homolog D [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p36.22
Genomic location:
Preferred name:
NM_015378.4(VPS13D):c.10818_10821del (p.Gly3607fs)
HGVS:
  • NC_000001.11:g.12373759_12373762del
  • NG_056877.1:g.148721_148724del
  • NM_015378.4:c.10818_10821delMANE SELECT
  • NM_018156.4:c.10743_10746del
  • NP_056193.2:p.Gly3607fs
  • NP_060626.2:p.Gly3582fs
  • LRG_1213t1:c.10818_10821del
  • LRG_1213:g.148721_148724del
  • LRG_1213p1:p.Gly3607fs
  • NC_000001.10:g.12433811_12433814del
  • NC_000001.10:g.12433814_12433817del
  • NM_015378.3:c.10818_10821delGGGA
Protein change:
G3582fs
Molecular consequence:
  • NM_015378.4:c.10818_10821del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_018156.4:c.10743_10746del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004392402Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Apr 19, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Recessive mutations in VPS13D cause childhood onset movement disorders.

Gauthier J, Meijer IA, Lessel D, Mencacci NE, Krainc D, Hempel M, Tsiakas K, Prokisch H, Rossignol E, Helm MH, Rodan LH, Karamchandani J, Carecchio M, Lubbe SJ, Telegrafi A, Henderson LB, Lorenzo K, Wallace SE, Glass IA, Hamdan FF, Michaud JL, Rouleau GA, et al.

Ann Neurol. 2018 Jun;83(6):1089-1095. doi: 10.1002/ana.25204. Epub 2018 Apr 10.

PubMed [citation]
PMID:
29518281

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004392402.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with VPS13D-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly3607Glnfs*29) in the VPS13D gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in VPS13D are known to be pathogenic (PMID: 29518281).

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

Last Updated: May 19, 2024