SLC28A1 p.Pro44=
c.132C>G · VCV4926276
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.237%, afr)
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 -8.4 | GERP -2.8 |
| Overall | ||
| CADD | 0.097 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.237%
African / African-American · 174/73,326 alleles
Filtering AF
0.208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.197%
Overall
0.0139%
216/1,554,896 alleles · rare
exomes 118/1,402,622 · genomes 98/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.237% | 421 |
| Remaining individualsnot grpmax-eligible | 0.0531% | 1,883 |
| Middle Eastern | 0.0168% | 5,946 |
| Admixed American | 0.00583% | 17,151 |
| South Asian | 0.00356% | 28,070 |
| European (non-Finnish) | 0.000261% | 382,973 |
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
- SLC28A1
- Protein
- p.Pro44=
- Coding
- c.132C>G
- MANE Select
- NM_004213
- Type
- single nucleotide variant
- Location
- chr15:84888807 (GRCh38)
- Gene constraint
- LOEUF 1.046 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.94
Similar variants
- SLC28A1 p.Arg147His Likely benign ★★ same type
- SLC28A1 p.Asn3= Benign ★★ same type
- SLC28A1 p.Gly210= Benign ★★ same type
- SLC28A1 p.Ala101Val Uncertain significance ★ ⚠ same type
- SLC28A1 p.Ala111Thr Uncertain significance ★ ⚠ same type
- SLC28A1 p.Ala201Thr Uncertain significance ★ ⚠ same type
- SLC28A1 p.Ala347Thr Uncertain significance ★ same type
- SLC28A1 p.Ala434Val 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/slc28a1-p-pro44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown