TTC7A p.Val475=
c.1425G>T · rs1679327755 · VCV1084565
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.51 | GERP -5, phastCons 0.99 |
| Overall | ||
| CADD | 4.191 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,179,996 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,614,160 alleles · very rare
exomes 3/1,461,824 · genomes 0/152,336 · 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
- TTC7A
- Protein
- p.Val475=
- Coding
- c.1425G>T
- MANE Select
- NM_020458
- dbSNP
- rs1679327755
- Type
- single nucleotide variant
- Location
- chr2:47021894 (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 p.Val475Ala Uncertain significance ★ ⚠ same residue
- TTC7A p.Val475Leu Uncertain significance ★ ⚠ same residue
- 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
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-val475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown