TULP1 p.Ala430=
c.1290G>A · rs146287182 · VCV1550223
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0287%, sas)
Conditions
1
inherited retinal dystrophy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -4.2 |
| Overall | ||
| CADD | 2.405 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0287%
South Asian · 25/87,212 alleles
Filtering AF
0.0199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.017%
Overall
0.00333%
53/1,590,884 alleles · ultra-rare
exomes 45/1,438,566 · genomes 8/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0287% | 3,488 |
| East Asian | 0.0161% | 6,226 |
| Remaining individualsnot grpmax-eligible | 0.00487% | 20,529 |
| African / African-American | 0.00402% | 24,853 |
| Admixed American | 0.00176% | 56,912 |
| European (non-Finnish) | 0.0012% | 83,488 |
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
- TULP1
- Protein
- p.Ala430=
- Coding
- c.1290G>A
- MANE Select
- NM_003322
- dbSNP
- rs146287182
- Type
- single nucleotide variant
- Location
- chr6:35503592 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.10 · 2 PDB
Similar variants
- TULP1 p.Ala430Val Uncertain significance ★★ ⚠ same residue
- TULP1 c.1496-6C>A Pathogenic/Likely pathogenic ★★ same condition
- TULP1 c.718+2T>C Pathogenic ★★ same condition
- TULP1 p.Arg361Ter Pathogenic ★★ same condition
- TULP1 p.Arg400Trp Pathogenic/Likely pathogenic ★★ same condition
- TULP1 p.Arg419Trp Pathogenic/Likely pathogenic ★★ same condition
- TULP1 p.Arg440Ter Pathogenic ★★ same condition
- TULP1 p.Asn349Lys Pathogenic/Likely pathogenic ★★ same condition
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/tulp1-p-ala430 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown