rs1555914719
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000273.3(GPR143):c.583T>C(p.Tyr195His) 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. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y195C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000273.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR143 | NM_000273.3 | c.583T>C | p.Tyr195His | missense_variant | 5/9 | ENST00000467482.6 | |
GPR143 | XM_005274541.4 | c.583T>C | p.Tyr195His | missense_variant | 5/9 | ||
GPR143 | XM_024452388.2 | c.331T>C | p.Tyr111His | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR143 | ENST00000467482.6 | c.583T>C | p.Tyr195His | missense_variant | 5/9 | 1 | NM_000273.3 | P1 | |
GPR143 | ENST00000447366.5 | c.331T>C | p.Tyr111His | missense_variant | 5/8 | 3 | |||
GPR143 | ENST00000431126.1 | c.331T>C | p.Tyr111His | missense_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD4 exome Cov.: 28
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 04, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at