TULP1 p.Thr46=
c.138G>A · rs868245971 · VCV1927778
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00207%, sas)
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 -9.6 | GERP -2.5 |
| Overall | ||
| CADD | 0.313 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00207%
South Asian · 1/48,422 alleles
Filtering AF
0.000138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0001%
Overall
0.000435%
6/1,378,268 alleles · very rare
exomes 6/1,226,094 · genomes 0/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00207% | 48,422 |
| European (non-Finnish) | 0.000469% | 213,048 |
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.Thr46=
- Coding
- c.138G>A
- MANE Select
- NM_003322
- dbSNP
- rs868245971
- Type
- single nucleotide variant
- Location
- chr6:35512232 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.10 · 2 PDB
- Residue 46
- the 'disordered' region
Similar variants
- TULP1 p.Thr46Met 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-thr46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown