ABCA4 p.Ile2113=
c.6339C>T · rs61750649 · VCV1541457
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00669%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.38 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.25 | loss · gain 0.24 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.18 | GERP -1.7 |
| Overall | ||
| CADD | 12.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,876 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000372%
6/1,614,056 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00669% | 14,959 |
| Admixed American | 0.00167% | 60,002 |
| African / African-American | 0.00133% | 74,928 |
| European (non-Finnish) | 8.47e-05% | 1,180,043 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ABCA4
- Protein
- p.Ile2113=
- Coding
- c.6339C>T
- MANE Select
- NM_000350
- dbSNP
- rs61750649
- Type
- single nucleotide variant
- Location
- chr1:94001049 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.96 · 8 PDB
- Residue 2113
- a UniProt-annotated variant site (in cord3; uncertain significance); a UniProt-annotated variant site (in stgd1; uncertain significance); a UniProt-annotated variant site (found in a patient with chorioretinal atrophy; uncertain significance); a UniProt-annotated variant site (found in a patient with macular dystrophy; uncertain significance); the abc transporter 2 domain; a UniProt-annotated variant site (in stgd1 and cord3; uncertain significance); a UniProt-annotated variant site (sequence variant); a UniProt-annotated variant site (in stgd1 and ffm; uncertain significance); a UniProt-annotated variant site (in stgd1; uncertain significance; also found in a patient with chorioretinal atrophy; uncertain significance); an α-helix
Similar variants
- ABCA4 p.Ile2113Met Likely pathogenic ★★ ⚠ same residue
- ABCA4 p.Ile2113Leu Uncertain significance ★ ⚠ same residue
- ABCA4 c.1937+1G>A Pathogenic ★★★ same type
- ABCA4 c.3328+2T>A Pathogenic ★★★ same type
- ABCA4 c.3523-1G>A Pathogenic ★★★ same type
- ABCA4 c.4253+43G>A Pathogenic ★★★ same type
- ABCA4 c.4254-1G>C Pathogenic ★★★ same type
- ABCA4 c.4352+1G>A Pathogenic ★★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/abca4-p-ile2113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown