rs104894163
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_001002295.2(GATA3):c.823T>A(p.Trp275Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W275L) has been classified as Pathogenic.
Frequency
Consequence
NM_001002295.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA3 | ENST00000379328.9 | c.823T>A | p.Trp275Arg | missense_variant | 4/6 | 1 | NM_001002295.2 | ENSP00000368632.3 | ||
GATA3 | ENST00000346208.4 | c.820T>A | p.Trp274Arg | missense_variant | 4/6 | 1 | ENSP00000341619.3 | |||
GATA3 | ENST00000461472.1 | c.442+5196T>A | intron_variant | 3 | ENSP00000515407.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hypoparathyroidism, deafness, renal disease syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2001 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at