rs869320785
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 8P and 1B. PP5_Very_StrongBP4
The NM_000350.3(ABCA4):c.4539+2028C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000394 in 152,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_000350.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152182Hom.: 0 Cov.: 33
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74346
ClinVar
Submissions by phenotype
not provided Pathogenic:4
This sequence change falls in intron 30 of the ABCA4 gene. It does not directly change the encoded amino acid sequence of the ABCA4 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (no rsID available, gnomAD 0.03%). This variant has been observed in individual(s) with Stargardt disease (PMID: 23918662). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 236116). Studies have shown that this variant results in pseudoexon inclusion, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 29526278). For these reasons, this variant has been classified as Pathogenic. -
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Published functional studies demonstrate a damaging effect with insertion of a 345 bp pseudoexon containing a stop codon, and the resulting transcript was subject to nonsense-mediated decay (Albert et al., 2018); This variant is associated with the following publications: (PMID: 26527198, 28118664, 23918662, 28771251, 29526278) -
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Severe early-childhood-onset retinal dystrophy Pathogenic:2
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 Stargardt disease 1 (MIM#248200). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Affected siblings can have variable age of onset and severity of disease (PMID:31522899). (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein due to the insertion of a retina-specific 345-nt pseudoexon (predicted protein change: p.Arg1514Leufs*36) (PMID: 29526278). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v3) (6 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times in Stargardt disease patients. Many of these patients have this variant in cis with c.302+68C>T (ClinVar, PMIDs: 32627976; 32307445; 25082829; 23918662). (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. By generating photoreceptor precursor cells (PPCs) from fibroblasts obtained from individuals with STGD1, it was demonstrated this deep-intronic variant results in a retina-specific 345-nt pseudoexon insertion (predicted protein change: p.Arg1514Leufs*36), likely due to the creation of exonic enhancers. This variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein. (PMID: 29526278). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
The ABCA4 c.4539+2028C>T variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PM2, PS3, PM3-S. Based on this evidence we have classified this variant as Pathogenic. -
Retinal dystrophy Pathogenic:2
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ABCA4-related disorder Pathogenic:1
The ABCA4 c.4539+2028C>T variant is predicted to interfere with splicing. This deep intronic variant has been reported in multiple individuals with Stargardt disease (see for examples: Table 1, Braun et al. 2013. PubMed ID: 23918662; Table S2, Lionel et al. 2017. PubMed ID: 28771251; Fadaie et al. 2021. PubMed ID: 34795310). RNA analysis of patient derived cells demonstrated that the c.4539+2028C>T variant causes the inclusion of a 345-nucleotide pseudo-exon (Albert et al. 2018. PubMed ID: 29526278; Huang et al. 2022. PubMed ID: 36209838). This variant is reported in 0.029% of alleles in individuals of European (Finnish) descent in gnomAD. This variant has been listed as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/236116/). Given the evidence, we interpret this variant as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at