12-76348214-G-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2PP3_ModeratePP5_Very_Strong
The NM_024685.4(BBS10):c.145C>T(p.Arg49Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,486 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_024685.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000484 AC: 12AN: 247886Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134698
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461302Hom.: 0 Cov.: 31 AF XY: 0.0000482 AC XY: 35AN XY: 726822
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome 10 Pathogenic:6
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The BBS10 c.145C>T (p.Arg49Trp) missense variant has been reported in nine studies in which it is found in at least 15 patients with Bardet-Biedl syndrome, including in four in a homozygous state and in 11 in a compound heterozygous state (Stoetzel et al. 2006; Hjortshøj et al. 2010; Muller et al. 2010; Bennouna-Greene et al. 2011; Chen et al. 2011; Imhoff et al. 2011; Schaefer et al. 2011; Lindstrand et al. 2014; Scheidecker et al. 2015). The p.Arg49Trp variant was absent from 192 control chromosomes and is reported at a frequency of 0.00009 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies demonstrated that the p.Arg49Trp variant was a null allele and failed to rescue morphant phenotypes seen in zebrafish embryos in which translation of the BBS10 protein was suppressed (Zaghloul et al. 2010). Based on the collective evidence, the p.Arg49Trp variant is considered to be pathogenic for Bardet-Biedl syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
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not provided Pathogenic:3
BBS10: PM3:Very Strong, PM2, PM5, PS3:Supporting -
Published functional studies demonstrate a damaging effect (Zaghloul et al., 2010); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30767287, 24746959, 20498079, 25982971, 16582908, 20472660, 22410627, 20080638, 20120035, 21344540, 30577886, 32686083, 33138063, 34426522) -
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Retinal dystrophy Pathogenic:2
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Inborn genetic diseases Pathogenic:1
The c.145C>T (p.R49W) alteration is located in exon 1 (coding exon 1) of the BBS10 gene. This alteration results from a C to T substitution at nucleotide position 145, causing the arginine (R) at amino acid position 49 to be replaced by a tryptophan (W). The alteration is not observed in healthy cohorts:_x000D_ Based on data from the NHLBI Exome Sequencing Project (ESP), the BBS10 c.145C>T alteration was not observed among 6,147 individuals tested. Allele frequency data for this nucleotide position are not currently available from the 1000 Genomes Project and the alteration is not currently listed in the Database of Single Nucleotide Polymorphisms (dbSNP)._x000D_ Though some variants may appear to be rare due to database-specific ethnic underrepresentation, rare missense alleles commonly exhibit a deleterious effect on protein function (Kryukov, 2007; Tennessen, 2012). IF USED, PULL THESE INTO REFERENCES:_x000D_ Kryukov GV, et al. (2007) Am J Hum Genet 80:727-739. Tennessen JA, et al. (2012) Science 337(64):64-69. The amino acid change has been observed in affected individuals:_x000D_ _x000D_ This missense change has been reported both in homozygous and compound heterozygous form in 8 families with BBS (Stoetzel, 2006; Chen, 2011; Imhoff, 2011; Deveault, 2011). The altered amino acid is conserved throughout evolution:_x000D_ The p.R49 amino acid is completely conserved in available vertebrate species. The alteration is predicted deleterious by in silico models:_x000D_ The p.R49W alteration is predicted to be probably damaging by Polyphen and deleterious by SIFT in silico analyses. Based on the available evidence, this alteration is classified as pathogenic. -
BBS10-related disorder Pathogenic:1
The BBS10 c.145C>T variant is predicted to result in the amino acid substitution p.Arg49Trp. This variant was reported in the homozygous or compound heterozygous state in multiple individuals with Bardet-Biedl syndrome (Stoetzel et al. 2006. PubMed ID: 16582908; Chen et al. 2011. PubMed ID: 21642631; Scheidecker et al. 2015. PubMed ID: 25982971; Jeziorny et al. 2020. PubMed ID: 33138063). Functional studies in a zebrafish model showed that the p.Arg49Trp substitution could impact normal protein function (Zaghloul et al. 2010. PubMed ID: 20498079, Supplementary Table 4). This variant is reported in 0.011% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -
High-frequency hearing impairment;C0024437:Macular degeneration;C0158734:Foot polydactyly;C0431904:Postaxial hand polydactyly;C0854723:Retinal dystrophy;C3714756:Intellectual disability Pathogenic:1
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Bardet-Biedl syndrome 1 Pathogenic:1
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Bardet-Biedl syndrome Pathogenic:1
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 49 of the BBS10 protein (p.Arg49Trp). This variant is present in population databases (rs768933093, gnomAD 0.01%). This missense change has been observed in individual(s) with Bardet-Biedl syndrome (PMID: 16582908, 20472660, 22410627, 25982971). ClinVar contains an entry for this variant (Variation ID: 225010). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt BBS10 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects BBS10 function (PMID: 20498079). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at