ClinVar Genomic variation as it relates to human health

The c.1674-1G>A variant in TCIRG1 has been reported in 3 unrelated patients affected with autosomal recessive infantile malignant osteopetrosis. Two of the patients were compound heterozygotes and one was homozygous (Frattini 2000). The variant has further been identified in 0.02% (2/8588) of European American chromosomes and 0.02% (1/4400) of African American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant occurs in the invariant region (+/- 1/2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. In summary, this variant meets our criteria to be classified as pathogenic (http://pcpgm.partners.org/LMM).

Variant summary: TCIRG1 c.1674-1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: One predicts the variant abolishes a 5 splicing donor site and another predicts the variant abolishes a 3 acceptor site. Three predict the variant weakens a 3 acceptor site. At least one publication reports experimental evidence that this variant results in aberrant splicing (Frattini_2000). The variant allele was found at a frequency of 0.00016 in 251008 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in TCIRG1 causing Osteopetrosis (0.00016 vs 0.0016), allowing no conclusion about variant significance. c.1674-1G>A has been reported in the literature in multiple individuals (both compound heterozygous and homozygous) affected with Osteopetrosis (e.g. Frattini_2000, Sobacchi_2001, Susani_2004). These data indicate that the variant is very likely to be associated with disease. Western blot analysis of EBV-immortalized cells from two compound heterozygous patients carrying the variant of interest and another variant showed no TCIRG1 protein expression (Frattini_2000). Six ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Western blot analysis did not detect mutant protein, supporting this variant results in a null allele (Frattini et al., 2000); Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 11532986, 30898715, 25525159, 10888887, 29431110, 10942435, 15300850, 31589614, 31949009, 24753205)

This sequence change affects an acceptor splice site in intron 14 of the TCIRG1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs139617644, gnomAD 0.03%). Disruption of this splice site has been observed in individuals with autosomal recessive osteopetrosis (PMID: 10888887, 15300850). This variant is also known as G10106A. ClinVar contains an entry for this variant (Variation ID: 189246). Studies have shown that disruption of this splice site results in abnormally spliced transcripts and introduces a premature termination codon (PMID: 10888887). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

The TCIRG1 c.1674-1G>A variant occurs in a canonical splice site (acceptor) and is therefore predicted to disrupt or distort the normal gene product. The c.1674-1G>A variant has been reported in three studies in which it is found in a total of 14 individuals with osteopetrosis including at least three homozygotes and 11 compound heterozygotes (Frattini et al. 2000; Sobacchi et al. 2001; Susani et al. 2004). The c.1674-1G>A variant was absent from 520 control chromosomes and is reported at a frequency of 0.000316 in the European (non-Finnish) population of the Genome Aggregation Database. Functional studies using RT-PCR revealed that the c.1674-1G>A variant causes abnormal splicing of the TCIRG1 transcript which was not detected in normal controls (Frattini et al. 2000). Western blot analysis of the cell lysates from two compound heterozygotes did not detect the presence of any TCIRG1 protein (Frattini et al. 2000). Based on the collective evidence and potential impact of splice site variants, the c.1674-1G>A is classified as pathogenic for osteopetrosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The c.1674-1G>A variant is located in a canonical splice-site, and it is predicted to alter gene function due to either exon skipping or nonsense-mediate decay – NMD, and the variant is present in a relevant exon to the transcript - PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 189246; PMID: 10888887; 11532986; 15300850) - PS4. The variant is present at low allele frequencies population databases (rs139617644 – gnomAD 0.001839%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The c.1674-1G>A was detected in trans with a pathogenic variant (PMID: 10888887) - PM3. In summary, the currently available evidence indicates that the variant is pathogenic.

NM_006019.3(TCIRG1):c.1674-1G>A is a canonical splice variant classified as pathogenic in the context of autosomal recessive osteopetrosis type 1. c.1674-1G>A has been observed in cases with relevant disease (PMID: 15300850). Functional assessments of this variant are not available in the literature. c.1674-1G>A has been observed in population frequency databases (gnomAD: NFE 0.03%). In summary, NM_006019.3(TCIRG1):c.1674-1G>A is a variant in a canonical splice site in a gene where loss of function is a known mechanism of disease, is predicted to disrupt protein function, and has been observed more frequently in cases with the relevant disease than in healthy populations. ​Please note: this variant was assessed in the context of healthy population screening.

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.016%). This variant was predicted to alter splicing and result in a loss or disruption of normal protein function. Multiple pathogenic loss-of-function variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000189246 / PMID: 10888887). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

The TCIRG1 c.1674-1G>A variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant (sometimes referred to as G10106A in the literature) has been reported in the homozygous and compound heterozygous states in several individuals with autosomal recessive osteopetrosis (see for example, Frattini et al. 2000. PubMed ID: 10888887; Capo et al. 2021. PubMed ID: 31949009). In vitro RNA studies confirmed that this variant disrupts splicing which leads to frameshift and no detectable protein (Frattini et al. 2000. PubMed ID: 10888887). This variant is reported in 0.032% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Variants that disrupt the consensus splice acceptor site in TCIRG1 are expected to be pathogenic. This variant is interpreted as pathogenic.