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NM_001378452.1(ITPR1):c.7660G>A (p.Gly2554Arg) AND Gillespie syndrome

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
May 9, 2018
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:
RCV000224995.6

Allele description [Variation Report for NM_001378452.1(ITPR1):c.7660G>A (p.Gly2554Arg)]

NM_001378452.1(ITPR1):c.7660G>A (p.Gly2554Arg)

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.7660G>A (p.Gly2554Arg)
Other names:
ITPR1, GLY2539ARG, 7615G-A
HGVS:
  • NC_000003.12:g.4814521G>A
  • NG_016144.1:g.326174G>A
  • NM_001099952.4:c.7516G>A
  • NM_001168272.2:c.7615G>A
  • NM_001378452.1:c.7660G>AMANE SELECT
  • NM_002222.7:c.7471G>A
  • NP_001093422.2:p.Gly2506Arg
  • NP_001161744.1:p.Gly2539Arg
  • NP_001161744.1:p.Gly2539Arg
  • NP_001365381.1:p.Gly2554Arg
  • NP_002213.5:p.Gly2491Arg
  • NC_000003.11:g.4856205G>A
  • NM_001168272.1:c.7615G>A
  • NM_002222.5:c.7471G>A
Protein change:
G2491R; GLY2539ARG
Links:
OMIM: 147265.0012; dbSNP: rs752281590
NCBI 1000 Genomes Browser:
rs752281590
Molecular consequence:
  • NM_001099952.4:c.7516G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001168272.2:c.7615G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378452.1:c.7660G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002222.7:c.7471G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Gillespie syndrome (GLSP)
Synonyms:
Aniridia, cerebellar ataxia, and mental deficiency; Aniridia-cerebellar ataxia-intellectual disability syndrome
Identifiers:
MONDO: MONDO:0008795; MedGen: C0431401; Orphanet: 1065; OMIM: 206700

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000281787OMIM
no assertion criteria provided
Pathogenic
(Jul 20, 2016) 		germlineliterature only

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

SCV000928365Laboratory of Medical Genetics, National & Kapodistrian University of Athens
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(May 9, 2018) 		de novoclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedde novoyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Restricted Repertoire of De Novo Mutations in ITPR1 Cause Gillespie Syndrome with Evidence for Dominant-Negative Effect.

McEntagart M, Williamson KA, Rainger JK, Wheeler A, Seawright A, De Baere E, Verdin H, Bergendahl LT, Quigley A, Rainger J, Dixit A, Sarkar A, López Laso E, Sanchez-Carpintero R, Barrio J, Bitoun P, Prescott T, Riise R, McKee S, Cook J, McKie L, Ceulemans B, et al.

Am J Hum Genet. 2016 May 5;98(5):981-992. doi: 10.1016/j.ajhg.2016.03.018. Epub 2016 Apr 21.

PubMed [citation]
PMID:
27108798
PMCID:
PMC4863663

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 OMIM, SCV000281787.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 5 unrelated patients with Gillespie syndrome (GLSP; 206700), McEntagart et al. (2016) identified heterozygosity for a de novo c.7615G-A transition (c.7615G-A, NM_001168272.1) in the ITPR1 gene (isoform 3), resulting in a gly2539-to-arg (G2539R) substitution in the transmembrane calcium ion transport domain.

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

From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV000928365.1

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

Description

PS3,PM6,PP2,PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 16, 2024