NM_001378452.1(ITPR1):c.7784G>C (p.Gly2595Ala) AND Spinocerebellar ataxia type 29

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 18, 2015
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:: RCV000235044.1

Allele description [Variation Report for NM_001378452.1(ITPR1):c.7784G>C (p.Gly2595Ala)]

NM_001378452.1(ITPR1):c.7784G>C (p.Gly2595Ala)

Genes:

LOC126806590:MED14-independent group 3 enhancer GRCh37_chr3:4855759-4856958 [Gene]
ITPR1:inositol 1,4,5-trisphosphate receptor type 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p26.1

Genomic location:

Preferred name:

NM_001378452.1(ITPR1):c.7784G>C (p.Gly2595Ala)

HGVS:

NC_000003.12:g.4815135G>C
NG_016144.1:g.326788G>C
NM_001099952.4:c.7640G>C
NM_001168272.2:c.7739G>C
NM_001378452.1:c.7784G>CMANE SELECT
NM_002222.7:c.7595G>C
NP_001093422.2:p.Gly2547Ala
NP_001161744.1:p.Gly2580Ala
NP_001365381.1:p.Gly2595Ala
NP_002213.5:p.Gly2532Ala
NC_000003.11:g.4856819G>C
NM_001099952.2:c.7640G>C

Protein change:

G2532A

Links:

dbSNP: rs869312685

NCBI 1000 Genomes Browser:

rs869312685

Molecular consequence:

NM_001099952.4:c.7640G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001168272.2:c.7739G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001378452.1:c.7784G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_002222.7:c.7595G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Spinocerebellar ataxia type 29 (SCA29)
Synonyms:: Cerebellar ataxia early-onset nonprogressive; CEREBELLAR ATAXIA, CONGENITAL NONPROGRESSIVE, AUTOSOMAL DOMINANT; Spinocerebellar ataxia 29, congenital nonprogressive
Identifiers:: MONDO: MONDO:0007298; MedGen: C1861732; Orphanet: 208513; OMIM: 117360

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000292354	Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine	criteria provided, single submitter (Gonzaga-Jauregui et al. (Cell Rep. 2015))	Likely pathogenic (Aug 18, 2015)	de novo	research	PubMed (3) [See all records that cite these PMIDs] 23806086, 24088041, 26257172

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000292354

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

criteria provided, single submitter

(Gonzaga-Jauregui et al. (Cell Rep. 2015))

Likely pathogenic
(Aug 18, 2015)

de novo

research

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	1	not provided	not provided	not provided	research

Citations

PubMed

Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy.

Lupski JR, Gonzaga-Jauregui C, Yang Y, Bainbridge MN, Jhangiani S, Buhay CJ, Kovar CL, Wang M, Hawes AC, Reid JG, Eng C, Muzny DM, Gibbs RA.

Genome Med. 2013;5(6):57. doi: 10.1186/gm461.

PubMed [citation]

PMID:: 23806086
PMCID:: PMC3706849

Clinical whole-exome sequencing for the diagnosis of mendelian disorders.

Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, et al.

N Engl J Med. 2013 Oct 17;369(16):1502-11. doi: 10.1056/NEJMoa1306555. Epub 2013 Oct 2.

PubMed [citation]

PMID:: 24088041
PMCID:: PMC4211433

See all PubMed Citations (3)

Details of each submission

From Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine, SCV000292354.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	PubMed (3)

Description

Likely pathogenic based on prediction scores (SIFT, MutationTaster). This de novo variant was identified in a patient with congenital ataxia who also had peripheral neuropathy.

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

Last Updated: Mar 26, 2023

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