TULP1 p.Ile367=
c.1101C>T · rs139648130 · VCV1137963
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0283%, amr)
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 -3.5 | GERP -3.9 |
| Overall | ||
| CADD | 4.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0283%
Admixed American · 17/60,016 alleles
Filtering AF
0.018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00836%
135/1,614,146 alleles · ultra-rare
exomes 120/1,461,874 · genomes 15/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0283% | 3,530 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.0083% | 12,041 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| South Asian | 0.00769% | 13,012 |
| African / African-American | 0.00533% | 18,761 |
| East Asian | 0.00446% | 22,435 |
| Finnishnot grpmax-eligible | 0.00156% | 64,038 |
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.Ile367=
- Coding
- c.1101C>T
- MANE Select
- NM_003322
- dbSNP
- rs139648130
- Type
- single nucleotide variant
- Location
- chr6:35505752 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.10 · 2 PDB
- Residue 367
- a β-strand
Similar variants
- TULP1 p.Ile367del Uncertain significance ★ same residue
- TULP1 c.1112+1G>A Likely pathogenic ★★ same type
- TULP1 c.1495+1G>A Pathogenic/Likely pathogenic ★★ same type
- TULP1 c.1496-6C>A Pathogenic/Likely pathogenic ★★ same type
- TULP1 c.718+2T>C Pathogenic ★★ same type
- TULP1 c.99+1G>A Pathogenic/Likely pathogenic ★★ same type
- TULP1 c.999+5G>C Pathogenic/Likely pathogenic ★★ same type
- TULP1 p.Arg311Gln Pathogenic/Likely 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/tulp1-p-ile367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown