chrX-9725612-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000273.3(GPR143):c.*134C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 506,144 control chromosomes in the GnomAD database, including 19,753 homozygotes. There are 41,194 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.36 ( 7896 hom., 11397 hem., cov: 22)
Exomes 𝑓: 0.24 ( 11857 hom. 29797 hem. )
Consequence
GPR143
NM_000273.3 3_prime_UTR
NM_000273.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.143
Genes affected
GPR143 (HGNC:20145): (G protein-coupled receptor 143) This gene encodes a protein that binds to heterotrimeric G proteins and is targeted to melanosomes in pigment cells. This protein is thought to be involved in intracellular signal transduction mechanisms. Mutations in this gene cause ocular albinism type 1, also referred to as Nettleship-Falls type ocular albinism, a severe visual disorder. A related pseudogene has been identified on chromosome Y. [provided by RefSeq, Dec 2009]
TBL1X (HGNC:11585): (transducin beta like 1 X-linked) The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This encoded protein is found as a subunit in corepressor SMRT (silencing mediator for retinoid and thyroid receptors) complex along with histone deacetylase 3 protein. This gene is located adjacent to the ocular albinism gene and it is thought to be involved in the pathogenesis of the ocular albinism with late-onset sensorineural deafness phenotype. Four transcript variants encoding two different isoforms have been found for this gene. This gene is highly similar to the Y chromosome TBL1Y gene. [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant X-9725612-G-A is Benign according to our data. Variant chrX-9725612-G-A is described in ClinVar as [Benign]. Clinvar id is 1294751.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR143 | NM_000273.3 | c.*134C>T | 3_prime_UTR_variant | 9/9 | ENST00000467482.6 | ||
GPR143 | XM_005274541.4 | c.*324C>T | 3_prime_UTR_variant | 9/9 | |||
GPR143 | XM_024452388.2 | c.*134C>T | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR143 | ENST00000467482.6 | c.*134C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_000273.3 | P1 | ||
TBL1X | ENST00000647060.1 | c.1554+10609G>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.362 AC: 39898AN: 110264Hom.: 7879 Cov.: 22 AF XY: 0.349 AC XY: 11355AN XY: 32566
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GnomAD4 exome AF: 0.238 AC: 94198AN: 395828Hom.: 11857 Cov.: 5 AF XY: 0.231 AC XY: 29797AN XY: 129124
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at