TTC12 p.Ser397=
c.1191G>C · rs201793229 · VCV2642378
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.191%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.009 | GERP -4.5, phastCons 0.023 |
| Overall | ||
| CADD | 2.975 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.191%
South Asian · 174/91,062 alleles
Filtering AF
0.168%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.159%
Overall
0.0117%
189/1,613,906 alleles · rare
exomes 181/1,461,680 · genomes 8/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.191% | 523 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,944 |
| East Asian | 0.00223% | 44,884 |
| Admixed American | 0.00167% | 60,006 |
| African / African-American | 0.00133% | 75,002 |
| European (non-Finnish) | 0.000254% | 393,286 |
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
- TTC12
- Protein
- p.Ser397=
- Coding
- c.1191G>C
- MANE Select
- NM_017868
- dbSNP
- rs201793229
- Type
- single nucleotide variant
- Location
- chr11:113350109 (GRCh38)
- Gene constraint
- LOEUF 0.934 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.27
- Residue 397
- a UniProt-annotated variant site (in cild45; reduced protein abundance; changed axonemal dynein complex assembly)
Similar variants
- TTC12 c.1247+24T>C Benign ★★ same type
- TTC12 c.1446+205T>A Benign ★★ same type
- TTC12 c.1446+55G>T Benign ★★ same type
- TTC12 c.1447-150C>T Benign ★★ same type
- TTC12 c.1546-62C>T Benign ★★ same type
- TTC12 c.1615-64G>A Benign ★★ same type
- TTC12 c.1717-79A>G Benign ★★ same type
- TTC12 c.1717-84G>A Benign ★★ 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/ttc12-p-ser397 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown