X-9725772-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000273.3(GPR143):c.1189G>T(p.Ala397Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000901 in 110,970 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000273.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR143 | NM_000273.3 | c.1189G>T | p.Ala397Ser | missense_variant | Exon 9 of 9 | ENST00000467482.6 | NP_000264.2 | |
GPR143 | XM_024452388.2 | c.937G>T | p.Ala313Ser | missense_variant | Exon 9 of 9 | XP_024308156.1 | ||
GPR143 | XM_005274541.4 | c.*164G>T | 3_prime_UTR_variant | Exon 9 of 9 | XP_005274598.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR143 | ENST00000467482.6 | c.1189G>T | p.Ala397Ser | missense_variant | Exon 9 of 9 | 1 | NM_000273.3 | ENSP00000417161.1 | ||
TBL1X | ENST00000647060.1 | c.1554+10769C>A | intron_variant | Intron 15 of 15 | ENSP00000495467.1 |
Frequencies
GnomAD3 genomes AF: 0.00000901 AC: 1AN: 110970Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33156
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.13e-7 AC: 1AN: 1095084Hom.: 0 Cov.: 29 AF XY: 0.00000277 AC XY: 1AN XY: 360532
GnomAD4 genome AF: 0.00000901 AC: 1AN: 110970Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33156
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 28, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with GPR143-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 397 of the GPR143 protein (p.Ala397Ser). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at