PROM1 p.Ala2=
c.6C>G · rs1169051313 · VCV1647663
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00504%, amr)
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 0.95 | GERP -4.5, phastCons 0.53 |
| Overall | ||
| CADD | 2.488 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00504%
Admixed American · 3/59,528 alleles
Filtering AF
0.00134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000671%
Overall
0.000249%
4/1,607,896 alleles · very rare
exomes 3/1,455,746 · genomes 1/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00504% | 19,843 |
| European (non-Finnish) | 8.5e-05% | 1,176,382 |
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
- PROM1
- Protein
- p.Ala2=
- Coding
- c.6C>G
- MANE Select
- NM_006017
- dbSNP
- rs1169051313
- Type
- single nucleotide variant
- Location
- chr4:16075901 (GRCh38)
- Gene constraint
- LOEUF 1.104 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.68
Similar variants
- PROM1 p.Ala2Val Uncertain significance ★ ⚠ same residue
- PROM1 c.1142-1G>A Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1301+1G>A Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1301+2T>C Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1578+1G>A Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1579-1G>C Pathogenic ★★ same type
- PROM1 c.1579-2A>C Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1984-1G>T Pathogenic ★★ 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/prom1-p-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown