ClinVar Genomic variation as it relates to human health

The c.117+4A>T variant in TCIRG1 has been reported in the homozygous state in at least 6 individuals and in the compound heterozygous state with another disease-causing variant in TCIRG1 in 1 individual with osteopetrosis and segregated with disease in 2 affected homozygous relatives from 1 family. This variant is presumed to likely be a founder variant in the Ashkenazi Jewish population where it is estimated to have a carrier frequency of 1 in 350 (Kornak 2000 PMID: 10942435, Susani 2004 PMID: 15300850, Mazzolari 2009 PMID: 19507210, Anderson 2015 PMID: 24989235). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 5462) and has also been identified in 0.057% (2/3468) of Ashkenazi Jewish chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). This variant is located in the 5' splice region. Computational tools predict and impact to splicing and in vitro functional studies using patient fibroblasts and minigene assays have shown that this variant activates an upstream cryptic splice site (also predicted by computational tools) which results in the deletion of 42 nucleotides from the transcript, resulting in the loss of 14 amino acid residues but preserving the integrity of the protein reading-frame (Kornak 2000 PMID: 10942435, Susani 2004 PMID: 15300850). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal recessive osteopetrosis. ACMG/AMP Criteria applied: PS3_Moderate, PM3, PP1_Moderate.

The c.117+4A>T intronic alteration consists of an A to T substitution 4 nucleotides after exon 2 (coding exon 1) of the TCIRG1 gene. Based on data from gnomAD, the T allele has an overall frequency of <0.01% (11/248134) total alleles studied. The highest observed frequency was 0.09% (9/9972) of Ashkenazi Jewish alleles. This alteration has been reported in the homozygous state in individuals with features of autosomal recessive osteopetrosis and was shown to segregate with disease in families (Anderson, 2015; Kornak, 2000). Haplotype analysis revealed that the carrier frequency in the Ashkenazi Jewish population is due to a single founder mutation (Anderson, 2015). Functional studies using RT-PCR analysis demonstrated that this alteration affected splicing, resulting in a 14 amino acid deletion located in the N-terminal, intracellular portion of the protein (Kornak, 2000). In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site. Based on the available evidence, this alteration is classified as pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with autosomal recessive osteopetrosis 1 (MIM#259700). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Patients may present with variable features (PMID: 17400532). (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. Minigene assay and RT-PCR show this variant results in the activation of an upstream cryptic splice site, causing an in-frame deletion of 14 amino acids in exon 2 and also exon 2 skipping (PMID: 15300850, 10942435, 24989235). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (11 heterozygotes, 0 homozygotes). (SP) 0311 - An alternative nucleotide change at the same position is present in gnomAD (v2) at a frequency of 0.0003269 (10 heterozygotes, 0 homozygotes). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic or likely pathogenic by multiple clinical laboratories in ClinVar, and has been observed in one compound heterozygous individual with osteopetrosis, and five unrelated homozygous individuals with osteopetrosis (PMID: 15300850, 10942435, 24989235). (SP) 1201 - Heterozygous variant detected in trans with a second pathogenic heterozygous variant (NM_006019.2(TCIRG1):c.2066G>A; p.(Trp689*)) in a recessive disease. (I) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Functional studies indicate that this splice site variant results int the activation of an upstream cryptic splice donor site and causes an in-frame deletion of exon 2 (Susani et al., 2004); This variant is associated with the following publications: (PMID: 30537558, 25046648, 15300850, 24989235, 10942435, 25525159)

This sequence change falls in intron 2 of the TCIRG1 gene. It does not directly change the encoded amino acid sequence of the TCIRG1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in the loss of 14 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs751881962, gnomAD 0.09%). This variant has been observed in individuals with osteopetrosis (PMID: 10942435, 15300850, 19507210, 24989235). This variant is also known as IVS2+4A>T. ClinVar contains an entry for this variant (Variation ID: 5462). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in the activation of a cryptic splice site in 2 (PMID: 10942435, 24989235). For these reasons, this variant has been classified as Pathogenic.

The TCIRG1 c.117+4A>T variant is predicted to interfere with splicing. This variant in the homozygous or compound heterozygous condition has been found in multiple patients with autosomal recessive osteopetrosis, and a functional study suggested that this variant causes splicing defects (Susani et al. 2004. PubMed ID: 15300850). This variant has been reported to be a founder mutation in the Ashkenazi Jewish population (Anderson et al. 2015. PubMed ID: 24989235). This variant is interpreted as pathogenic.