ALMS1 p.Ala486fs
c.1457_1459delinsTT · VCV4292613
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Alstrom syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 8 of 23 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.041 | GERP -4.4, phastCons 0.088 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ALMS1
- Protein
- p.Ala486fs
- Coding
- c.1457_1459delinsTT
- MANE Select
- NM_001378454
- Type
- Indel
- Location
- chr2:73447984 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Disease context
Alstrom syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Alström syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- ALMS1 p.Ala486= Likely benign ★ same residue
- ALMS1 p.Gln3434fs Pathogenic ★★ same condition
- ALMS1 p.Glu2706fs Likely pathogenic ★★ same condition
- ALMS1 p.Gly613Asn Uncertain significance ★★ same condition
- ALMS1 p.His575delinsProSer Uncertain significance ★★ same condition
- ALMS1 c.12362+16_12362+27delinsTGAGTTTGTG Benign/Likely benign ★★ same condition
- ALMS1 p.Gln63fs Likely pathogenic ★ same condition
- ALMS1 p.Gly1555Ter 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-ala486fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown