NM_002049.3(GATA1):c.89C>G (p.Ser30Ter) AND multiple conditions

Clinical significance:Pathogenic (Last evaluated: May 16, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000552766.1

Allele description [Variation Report for NM_002049.3(GATA1):c.89C>G (p.Ser30Ter)]

NM_002049.3(GATA1):c.89C>G (p.Ser30Ter)

Gene:
GATA1:GATA binding protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.23
Genomic location:
Preferred name:
NM_002049.3(GATA1):c.89C>G (p.Ser30Ter)
HGVS:
  • NC_000023.11:g.48791198C>G
  • NG_008846.2:g.9625C>G
  • NM_002049.3:c.89C>G
  • NP_002040.1:p.Ser30Ter
  • LRG_559t1:c.89C>G
  • LRG_559:g.9625C>G
  • LRG_559p1:p.Ser30Ter
  • NC_000023.10:g.48649605C>G
Protein change:
S30*
Links:
dbSNP: rs1557020021
NCBI 1000 Genomes Browser:
rs1557020021
Molecular consequence:
  • NM_002049.3:c.89C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Thrombocytopenia, X-linked, with or without dyserythropoietic anemia (XLTDA)
Identifiers:
MONDO: MONDO:0010308; MedGen: C3550789; Orphanet: 67044; OMIM: 300367
Name:
Diamond-Blackfan anemia (DBA)
Synonyms:
ANEMIA, CONGENITAL HYPOPLASTIC, OF BLACKFAN AND DIAMOND; Blackfan Diamond syndrome; Anemia congenital erythroid hypoplastic; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015253; MeSH: D029503; MedGen: C1260899; Orphanet: 124; OMIM: PS105650; Human Phenotype Ontology: HP:0004810

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000640017Invitaecriteria provided, single submitter
Pathogenic
(May 16, 2017)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000640017.1

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

Description

This sequence change creates a premature translational stop signal at codon 30 (p.Ser30*) of the GATA1 gene. It is expected to result in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with a GATA1-related disease. Although this variant is expected to create a premature translational stop signal at codon 30 of the GATA1 protein, studies have shown that translation can initiate at codon 84, resulting in the formation of a shorter protein (GATA1s) that lacks the transactivation domain within the first 83 amino acids. Variants in GATA1 (c. 332G>C, c.220+1delG) that result in the expression of the GATA1s isoform, through skipping of the initiating methionine-containing exon, have been reported in individuals with Diamond Blackfan anemia (PMID: 16783379, 22706301, 24766296). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 8, 2021

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