FTCD p.Pro31=
c.93G>A · VCV4946734
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0112%, eas)
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 -20 | GERP -2.8 |
| Overall | ||
| CADD | 0.436 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0112%
East Asian · 5/44,836 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.0013%
21/1,611,660 alleles · ultra-rare
exomes 16/1,459,412 · genomes 5/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0112% | 8,967 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,593 |
| South Asian | 0.0044% | 22,752 |
| Admixed American | 0.00334% | 29,979 |
| African / African-American | 0.00267% | 37,453 |
| European (non-Finnish) | 0.000339% | 294,939 |
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
- FTCD
- Protein
- p.Pro31=
- Coding
- c.93G>A
- MANE Select
- NM_206965
- Type
- single nucleotide variant
- Location
- chr21:46154294 (GRCh38)
- Gene constraint
- LOEUF 1.61 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 95.30
- Residue 31
- the 'formiminotransferase n-subdomain' region
Similar variants
- FTCD p.Pro31Leu Uncertain significance ★★ ⚠ same residue
- FTCD p.Arg255Ter Pathogenic ★★ same type
- FTCD p.Arg71Ter Pathogenic/Likely pathogenic ★★ same type
- FTCD p.Leu536Ter Pathogenic/Likely pathogenic ★★ same type
- FTCD p.Ala108Thr Uncertain significance ★★ ⚠ same type
- FTCD p.Ala159Val Uncertain significance ★★ ⚠ same type
- FTCD p.Ala352Val Uncertain significance ★★ ⚠ same type
- FTCD p.Ala361Val Uncertain significance ★★ 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/ftcd-p-pro31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown