ClinVar Genomic variation as it relates to human health

Variant summary: BBS12 c.1531_1539delCAGATGCAA (p.Gln511_Gln513del) results in an in-frame deletion that is predicted to remove three amino acids from the encoded protein. The variant allele was found at a frequency of 4e-05 in 251428 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in BBS12 causing Bardet-Biedl Syndrome (4e-05 vs 0.00076), allowing no conclusion about variant significance. c.1531_1539delCAGATGCAA has been reported in the literature in individuals affected with Bardet-Biedl Syndrome (Stoetzel_2006, Hjortshj_2010, Manara_2019). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and this variant affects protein function (Zaghloul_2010). The following publications have been ascertained in the context of this evaluation (PMID: 21463199, 31964843, 20120035, 30718709, 31196119, 20648243, 17160889, 20498079). Seven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic (n=2) and likely pathogenic (n=5). Based on the evidence outlined above, the variant was classified as likely pathogenic.

This variant, c.1531_1539del, results in the deletion of 3 amino acid(s) of the BBS12 protein (p.Gln511_Gln513del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs752762669, gnomAD 0.007%). This variant has been observed in individual(s) with Bardet-Biedl syndrome (PMID: 17160889, 20120035; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 434492). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects BBS12 function (PMID: 20498079). For these reasons, this variant has been classified as Pathogenic.

In-frame deletion of 3 amino acids in a non-repeat region; Published functional studies in zebrafish suggest a damaging effect (PMID: 20498079); In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 30718709, 20120035, 17160889, 31196119, 20498079, 36938085, 31964843)

The BBS12 c.1531_1539del9 variant is predicted to result in an in-frame deletion (p.Gln511_Gln513del). This variant was reported in individuals with Bardet-Biedl syndrome (Stoetzel et al 2007. PubMed ID: 17160889; Hjortshøj et al. 2010. PubMed ID: 20120035). Functional studies using zebrafish suggest that this variant is deleterious (Supp. Table 4, Zaghloul et al. 2010. PubMed ID: 20498079). This variant is reported in 0.0085% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as likely pathogenic.