TTC19 c.*1003C>T
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000441%, nfe)
Conditions
1
mitochondrial complex III deficiency nuclear type 2
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 -0.25 | GERP -2.8 |
| Overall | ||
| CADD | 5.565 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000441%
European (non-Finnish) · 1/226,780 alleles
Overall
0.00022%
1/453,912 alleles · very rare
exomes 0/301,786 · genomes 1/152,126 · joint denominator
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.*1003C>T
- MANE Select
- NM_017775
- dbSNP
- rs1971668947
- Type
- single nucleotide variant
- Location
- chr17:16028525 (GRCh38)
- Gene constraint
- LOEUF 1.049 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.28
Similar variants
- TTC19 p.Gln195Ter Pathogenic/Likely pathogenic ★★ same condition
- TTC19 p.Leu185Pro Pathogenic/Likely pathogenic ★★ same condition
- TTC19 p.Leu219Ter Pathogenic ★★ same condition
- TTC19 c.581+4A>C Uncertain significance ★★ same condition
- TTC19 c.994+3A>T Uncertain significance ★★ same condition
- TTC19 p.Ala122Thr Uncertain significance ★★ ⚠ same condition
- TTC19 p.Ala263Ser Uncertain significance ★★ ⚠ same condition
- TTC19 p.Arg102Gly 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-star-1003c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown