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NM_001002295.2(GATA3):c.1058G>C (p.Arg353Thr) AND Hypoparathyroidism, deafness, renal disease syndrome

Germline classification:
Likely pathogenic (2 submissions)
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:
RCV000709930.2

Allele description [Variation Report for NM_001002295.2(GATA3):c.1058G>C (p.Arg353Thr)]

NM_001002295.2(GATA3):c.1058G>C (p.Arg353Thr)

Gene:
GATA3:GATA binding protein 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10p14
Genomic location:
Preferred name:
NM_001002295.2(GATA3):c.1058G>C (p.Arg353Thr)
HGVS:
  • NC_000010.11:g.8073746G>C
  • NG_015859.1:g.24043G>C
  • NM_001002295.2:c.1058G>CMANE SELECT
  • NM_002051.3:c.1055G>C
  • NP_001002295.1:p.Arg353Thr
  • NP_002042.1:p.Arg352Thr
  • NC_000010.10:g.8115709G>C
  • NM_001002295.1:c.1058G>C
Protein change:
R352T
Links:
dbSNP: rs1564405163
NCBI 1000 Genomes Browser:
rs1564405163
Molecular consequence:
  • NM_001002295.2:c.1058G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002051.3:c.1055G>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Name:
Hypoparathyroidism, deafness, renal disease syndrome (HDRS)
Synonyms:
Barakat syndrome; Hypoparathyroidism, sensorineural deafness, and renal dysplasia; HDR syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007797; MedGen: C1840333; Orphanet: 2237; OMIM: 146255

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000840279GenomeConnect, ClinGen
no classification provided
not providedpaternalphenotyping only

SCV000924307University of Iowa Renal Genetics Clinic, University of Iowa
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineresearch, clinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedpaternalunknownnot providednot providednot providednot providednot providedphenotyping only
Caucasiangermlineyes2not providednot providednot providednot providedresearch, 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 GenomeConnect, ClinGen, SCV000840279.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedphenotyping onlynot provided

Description

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalunknownnot providednot providedvalidationnot providednot providednot providednot provided

From University of Iowa Renal Genetics Clinic, University of Iowa, SCV000924307.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian1not providednot providedresearch PubMed (1)
2Caucasian1not providednot providedclinical testing PubMed (1)

Description

The Arg353Thr variant was identified within 1 Caucasian family. One individual has a clinical diagnosis of HDR (Barakat) syndrome and a second individual has a suspected history of HDR syndrome. This variant is ultra rare (PM2), predicted pathogenic (PP3), cosegregates with disease in 2 family members (PP1), is a novel missense change at an amino acid residue with a different missense change (Arg353Ser) which has been reported pathogenic (PM5), and the variant is in a gene that is highly specific for the family phenotype (PP4).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided
2germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Aug 5, 2023