TULP1 p.Leu8=
c.24C>A · rs764915724 · VCV1093028
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.27%, eas)
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 0.34 | GERP -3.7, phastCons 0.98 |
| Overall | ||
| CADD | 7.408 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.27%
East Asian · 121/44,870 alleles
Filtering AF
0.231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.216%
Overall
0.00763%
123/1,612,852 alleles · rare
exomes 120/1,460,960 · genomes 3/151,892 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.27% | 371 |
| Admixed American | 0.00167% | 59,974 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,454 |
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.Leu8=
- Coding
- c.24C>A
- MANE Select
- NM_003322
- dbSNP
- rs764915724
- Type
- single nucleotide variant
- Location
- chr6:35512835 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.10 · 2 PDB
- Residue 8
- the 'disordered' region
Similar variants
- 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
- TULP1 p.Gln401Ter 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-leu8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown