TTC19 c.200G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0288%, eas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.01 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.95 | GERP -1.6 |
| Non-coding constraint | Z 3.07 | 1 kb window · o/e 0.79 · regional · uncalibrated |
| Overall | ||
| CADD | 8.498 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0288%
East Asian · 12/41,640 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.013%
Overall
0.00116%
18/1,557,062 alleles · ultra-rare
exomes 13/1,404,796 · genomes 5/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0288% | 3,470 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,390 |
| South Asian | 0.00118% | 84,954 |
| European (non-Finnish) | 0.000348% | 287,770 |
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
- TTC19
- Coding
- c.200G>A
- MANE Select
- NM_017775
- Type
- single nucleotide variant
- Location
- chr17:15999685 (GRCh38)
- Gene constraint
- LOEUF 1.049 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.28
Similar variants
- TTC19 p.Ala200Val Uncertain significance ★★ ⚠ same condition
- TTC19 p.Ala263Ser Uncertain significance ★★ ⚠ same condition
- TTC19 p.Ala85Val Uncertain significance ★★ ⚠ same condition
- TTC19 p.Arg102Gly Uncertain significance ★★ ⚠ same condition
- TTC19 p.Arg124His Uncertain significance ★★ ⚠ same condition
- TTC19 p.Arg294Cys Uncertain significance ★★ ⚠ same condition
- TTC19 p.Ile206Met Uncertain significance ★★ ⚠ same condition
- TTC19 p.Lys160Gln Uncertain significance ★★ ⚠ 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/ttc19-c-200g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown