NM_005029.4:c.640_656delGCCCTGCAGGGCCTGGG
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 12P and 4B. PVS1_StrongPP5_Very_StrongBS2
The NM_005029.4(PITX3):c.640_656delGCCCTGCAGGGCCTGGG(p.Ala214ArgfsTer42) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000397 in 1,510,390 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_005029.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PITX3 | NM_005029.4 | c.640_656delGCCCTGCAGGGCCTGGG | p.Ala214ArgfsTer42 | frameshift_variant | Exon 4 of 4 | ENST00000370002.8 | NP_005020.1 | |
PITX3 | XM_047425352.1 | c.640_656delGCCCTGCAGGGCCTGGG | p.Ala214ArgfsTer42 | frameshift_variant | Exon 3 of 3 | XP_047281308.1 | ||
GBF1 | NM_001391923.1 | c.-149_-133delCAGGGCCCCAGGCCCTG | 5_prime_UTR_variant | Exon 1 of 40 | NP_001378852.1 | |||
GBF1 | NM_001391924.1 | c.-287_-271delCAGGGCCCCAGGCCCTG | 5_prime_UTR_variant | Exon 1 of 41 | NP_001378853.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151964Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000747 AC: 8AN: 107136Hom.: 0 AF XY: 0.000118 AC XY: 7AN XY: 59242
GnomAD4 exome AF: 0.0000412 AC: 56AN: 1358426Hom.: 0 AF XY: 0.0000433 AC XY: 29AN XY: 669416
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151964Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74220
ClinVar
Submissions by phenotype
Cataract 11 multiple types Pathogenic:1
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not provided Pathogenic:1
Experimental studies have shown that this premature translational stop signal affects PITX3 function (PMID: 30816539). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. This sequence change creates a premature translational stop signal (p.Ala214Argfs*42) in the PITX3 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 89 amino acid(s) of the PITX3 protein. This variant is present in population databases (no rsID available, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with congenital cataracts and/or Peter's anomalies (PMID: 30816539; Invitae). ClinVar contains an entry for this variant (Variation ID: 468252). -
Anterior segment dysgenesis 1 Pathogenic:1
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 PITX3-related anterior segment dysgenesis and cataracts. (I) 0108 - This gene is associated with both recessive and dominant disease. This gene has mostly been associated with dominant disease, although rare cases of recessive inheritance have been reported, with homozygous individuals having a more severe phenotype (PMID: 21836522, PMID: 30816539, PMID: 29405783). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 30816539). (I) 0115 - Variants in this gene are known to have variable expressivity. A wide range of interfamilial and intrafamilial phenotypic variability has been reported. (PMID: 29405783). (I) 0205 - Variant is predicted to result in a truncated protein (premature termination codon is NOT located at least 54 nucleotides upstream of the final exon-exon junction) with less than 1/3 of the protein sequence affected. (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 (8 heterozygotes, 0 homozygotes). (SP) 0600 - Variant is predicted to lose the OAR domain. The majority of reported pathogenic variants in PITX3 are predicted to result in the disruption of the OAR domain (PMID: 30894134). (I) 0702 - Other variants predicted to result in a truncated protein comparable to the one identified in this case have strong previous evidence for pathogenicity (ClinVar, PMID: 32830442). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has been previously reported in a homozygous patient with anterior segment dysgenesis and microphthalmia (PMID: 21836522) and heterozygous in at least four unrelated patients with congenital cataracts or Peters Anomaly (PMID: 30816539, PMID: 31848469, PMID: 33923544, PMID: 33304895). This variant has also been reported as a VUS in ClinVar. (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies indicated that the mutant protein retained a nuclear localisation pattern but resulted in decreased transactivation activity (PMID: 30816539). (SP) 1206 - This variant has been shown to be paternally inherited. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at