ALMS1 p.Pro2157=
c.6471A>G · rs2466109203 · VCV3046145
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
ALMS1-related disorder
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 4.1 | GERP 0.87, phastCons 1 |
| Overall | ||
| CADD | 6.674 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ALMS1
- Protein
- p.Pro2157=
- Coding
- c.6471A>G
- MANE Select
- NM_001378454
- dbSNP
- rs2466109203
- Type
- single nucleotide variant
- Location
- chr2:73452998 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2157
- the '34 x 47 aa approximate tandem repeat' region
Disease context
ALMS1-related disorder
Similar variants
- ALMS1 c.12299-1G>A Likely pathogenic ★★ same condition
- ALMS1 p.Arg2669Ter Pathogenic ★★ same condition
- ALMS1 p.Arg2721Ter Pathogenic ★★ same condition
- ALMS1 p.Arg2927Ter Pathogenic ★★ same condition
- ALMS1 p.Arg3658Ter Pathogenic ★★ same condition
- ALMS1 p.Arg680Ter Pathogenic ★★ same condition
- ALMS1 p.Gln119Ter Pathogenic/Likely pathogenic ★★ same condition
- ALMS1 p.Gln123Ter Pathogenic/Likely pathogenic ★★ same condition
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/alms1-p-pro2157 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown