TTC7A p.Pro850=
c.2550C>T · rs780449127 · VCV1157182
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00746%, nfe)
Conditions
1
multiple intestinal atresia
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 1.1 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 10.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00746%
European (non-Finnish) · 88/1,179,972 alleles
Filtering AF
0.00615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00573%
Overall
0.00577%
93/1,612,872 alleles · very rare
exomes 86/1,460,636 · genomes 7/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00746% | 13,409 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,600 |
| African / African-American | 0.00133% | 74,916 |
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
- TTC7A
- Protein
- p.Pro850=
- Coding
- c.2550C>T
- MANE Select
- NM_020458
- dbSNP
- rs780449127
- Type
- single nucleotide variant
- Location
- chr2:47073896 (GRCh38)
- Gene constraint
- LOEUF 1.198 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 84.59
Similar variants
- TTC7A c.1288-1G>T Pathogenic/Likely pathogenic ★★ same condition
- TTC7A c.1641+1G>A Likely pathogenic ★★ same condition
- TTC7A c.2018-1G>C Pathogenic/Likely pathogenic ★★ same condition
- TTC7A p.Arg138Ter Pathogenic/Likely pathogenic ★★ same condition
- TTC7A p.Arg358Ter Pathogenic/Likely pathogenic ★★ same condition
- TTC7A p.Arg405Ter Pathogenic/Likely pathogenic ★★ same condition
- TTC7A p.Cys623Ter Pathogenic ★★ same condition
- TTC7A p.Gln526Ter Pathogenic ★★ 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/ttc7a-p-pro850 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown