NM_033305.3(VPS13A):c.9109C>T (p.Arg3037Ter) AND Chorea-acanthocytosis

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Apr 18, 2022
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:: RCV001333419.5

Allele description [Variation Report for NM_033305.3(VPS13A):c.9109C>T (p.Arg3037Ter)]

NM_033305.3(VPS13A):c.9109C>T (p.Arg3037Ter)

Gene:

VPS13A:vacuolar protein sorting 13 homolog A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q21.2

Genomic location:

Preferred name:

NM_033305.3(VPS13A):c.9109C>T (p.Arg3037Ter)

HGVS:

NC_000009.12:g.77382007C>T
NG_008931.1:g.209563C>T
NM_001018037.2:c.8992C>T
NM_001018038.3:c.9109C>T
NM_015186.4:c.9109C>T
NM_033305.3:c.9109C>TMANE SELECT
NP_001018047.1:p.Arg2998Ter
NP_001018048.1:p.Arg3037Ter
NP_056001.1:p.Arg3037Ter
NP_150648.2:p.Arg3037Ter
NC_000009.11:g.79996923C>T
NM_033305.2:c.9109C>T

Protein change:

R2998*

Links:

dbSNP: rs199807227

NCBI 1000 Genomes Browser:

rs199807227

Molecular consequence:

NM_001018037.2:c.8992C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001018038.3:c.9109C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_015186.4:c.9109C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_033305.3:c.9109C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Chorea-acanthocytosis
Synonyms:: Choreoacanthocytosis; Acanthocytosis with neurologic disorder; Levine-Critchley syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008695; MedGen: C0393576; Orphanet: 2388; OMIM: 200150

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001452564	Natera, Inc.	no assertion criteria provided	Pathogenic (Sep 16, 2020)	germline	clinical testing
SCV002808740	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 18, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005091451	Solve-RD Consortium	no assertion criteria provided	Likely pathogenic (Jun 1, 2022)	inherited	provider interpretation

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001452564

Natera, Inc.

no assertion criteria provided

Pathogenic
(Sep 16, 2020)

germline

clinical testing

SCV002808740

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 18, 2022)

unknown

clinical testing

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

SCV005091451

Solve-RD Consortium

no assertion criteria provided

Likely pathogenic
(Jun 1, 2022)

inherited

provider interpretation

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	provider interpretation
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

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 Natera, Inc., SCV001452564.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002808740.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Solve-RD Consortium, SCV005091451.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	provider interpretation	not provided

Description

Variant confirmed as disease-causing by referring clinical team

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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