TULP3 p.Thr115=
c.345C>G · rs775538452 · VCV2642575
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.001 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -3 |
| Overall | ||
| CADD | 0.234 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,078 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000991%
16/1,614,058 alleles · very rare
exomes 15/1,461,822 · genomes 1/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,769 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
| European (non-Finnish) | 0.000932% | 107,274 |
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
- TULP3
- Protein
- p.Thr115=
- Coding
- c.345C>G
- MANE Select
- NM_003324
- dbSNP
- rs775538452
- Type
- single nucleotide variant
- Location
- chr12:2922353 (GRCh38)
- Gene constraint
- LOEUF 1.059 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.51 · 1 PDB
- Residue 115
- the 'disordered' region; a UniProt-annotated variant site (in hrcdf)
Similar variants
- TULP3 p.Glu45Asp Uncertain significance ★★ ⚠ same type
- TULP3 c.*1187G>T Benign ★★ same type
- TULP3 p.Ala296Glu Benign ★★ same type
- TULP3 p.Arg380His Benign ★★ same type
- TULP3 c.492+1G>A Likely pathogenic ★ same type
- TULP3 c.809+2T>C Pathogenic ★ same type
- TULP3 c.810-1G>C Likely pathogenic ★ same type
- TULP3 c.*1102G>C Uncertain significance ★ 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/tulp3-p-thr115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown