SFTPC p.Val31=
c.93G>A · VCV4899704
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0176%, sas)
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 5 | GERP 0.11, phastCons 1 |
| Overall | ||
| CADD | 8.646 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0176%
South Asian · 16/91,082 alleles
Filtering AF
0.011%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.00105%
17/1,614,218 alleles · ultra-rare
exomes 17/1,461,850 · genomes 0/152,368 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0176% | 5,693 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
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
- SFTPC
- Protein
- p.Val31=
- Coding
- c.93G>A
- MANE Select
- NM_001317778
- Type
- single nucleotide variant
- Location
- chr8:22162624 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.71 · 3 PDB
Similar variants
- SFTPC c.435+2T>C Pathogenic/Likely pathogenic ★★ same type
- SFTPC p.Ile73Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- SFTPC p.Leu110Pro Pathogenic/Likely pathogenic ★★ same type
- SFTPC p.Leu55Phe Likely pathogenic ★★ ⚠ same type
- SFTPC c.*193C>A Uncertain significance ★★ same type
- SFTPC p.Gly4Ser Uncertain significance ★★ ⚠ same type
- SFTPC p.Ile50Met Uncertain significance ★★ ⚠ same type
- SFTPC p.Leu45Pro 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/sftpc-p-val31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown