SFTPC p.Val44del
c.117GGT[4] · rs752666425 · VCV2503267
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0198%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -1.1, phastCons 0.001 |
| Overall | ||
| CADD | 17.83 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (GTG)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0198%
South Asian · 18/91,076 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00273%
44/1,612,982 alleles · ultra-rare
exomes 43/1,460,810 · genomes 1/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0198% | 5,060 |
| Finnishnot grpmax-eligible | 0.00313% | 31,968 |
| European (non-Finnish) | 0.00195% | 51,268 |
| African / African-American | 0.00134% | 74,894 |
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.Val44del
- Coding
- c.117GGT[4]
- MANE Select
- NM_001317778
- dbSNP
- rs752666425
- Type
- Microsatellite
- Location
- chr8:22162646 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.71 · 3 PDB
Similar variants
- SFTPC p.Val44_Leu45insVal Uncertain significance ★ same residue
- SFTPC p.Val44_Leu45insValVal Likely benign ★ same residue
- SFTPC p.Glu159fs Likely pathogenic ★ same type
- SFTPC c.435+1GT[5] Likely benign ★ same type
- SFTPC c.435+1GT[7] Likely benign ★ 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-val44del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown