rs190174009
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000273.3(GPR143):c.1120+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000243 in 1,125,567 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 74 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., 38 hem., cov: 23)
Exomes 𝑓: 0.00014 ( 0 hom. 36 hem. )
Consequence
GPR143
NM_000273.3 intron
NM_000273.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.421
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant X-9739469-G-A is Benign according to our data. Variant chrX-9739469-G-A is described in ClinVar as [Benign]. Clinvar id is 255710.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00118 (132/112278) while in subpopulation AFR AF= 0.00423 (131/30984). AF 95% confidence interval is 0.00364. There are 0 homozygotes in gnomad4. There are 38 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd4 at 38 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR143 | NM_000273.3 | c.1120+16C>T | intron_variant | ENST00000467482.6 | |||
LOC105373126 | XR_950507.2 | n.1620+750G>A | intron_variant, non_coding_transcript_variant | ||||
GPR143 | XM_005274541.4 | c.1120+16C>T | intron_variant | ||||
GPR143 | XM_024452388.2 | c.868+16C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR143 | ENST00000467482.6 | c.1120+16C>T | intron_variant | 1 | NM_000273.3 | P1 | |||
TBL1X | ENST00000647060.1 | c.1555-1313G>A | intron_variant | ||||||
GPR143 | ENST00000487206.1 | n.235+16C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00118 AC: 132AN: 112228Hom.: 0 Cov.: 23 AF XY: 0.00108 AC XY: 37AN XY: 34394
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GnomAD3 exomes AF: 0.000393 AC: 65AN: 165422Hom.: 0 AF XY: 0.000209 AC XY: 11AN XY: 52728
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GnomAD4 exome AF: 0.000140 AC: 142AN: 1013289Hom.: 0 Cov.: 22 AF XY: 0.000119 AC XY: 36AN XY: 302293
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GnomAD4 genome ? AF: 0.00118 AC: 132AN: 112278Hom.: 0 Cov.: 23 AF XY: 0.00110 AC XY: 38AN XY: 34454
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at