Is ALG9 p.Ala175fs (c.522del) pathogenic?

ALG9 p.Ala175fs (c.522del) is classified Likely pathogenic in ALG9 (ClinVar, Single submitter, 2 submitters; last evaluated 2026-01-26). Absent from gnomAD; Associated with ALG9-associated autosomal dominant polycystic kidney disease.

What condition is associated with ALG9 p.Ala175fs (c.522del)?

ALG9 p.Ala175fs (c.522del) is associated with ALG9-associated autosomal dominant polycystic kidney disease (ClinVar).

How common is ALG9 p.Ala175fs (c.522del) in the general population?

ALG9 p.Ala175fs (c.522del) is absent from gnomAD (gnomAD).

How is Autosomal dominant polycystic kidney disease inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

ALG9 p.Ala175fs

c.522del · rs2497476150 · VCV2633266

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ALG9-associated autosomal dominant polycystic kidney disease

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 5 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 1.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ALG9
Protein: p.Ala175fs
Coding: c.522del
MANE Select: NM_024740
dbSNP: rs2497476150
Type: Deletion
Location: chr11:111860590 (GRCh38)
Gene constraint: LOEUF 0.853 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.35 · 2 PDB

Full ALG9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG9-associated autosomal dominant polycystic kidney disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant polycystic kidney disease (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

ALG9 p.Arg409fs Pathogenic/Likely pathogenic ★★ same condition
ALG9 p.Ala175Thr Uncertain significance ★ ⚠ same residue
ALG9 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same condition
ALG9 p.Gln594Ter Uncertain significance ★★ same condition
ALG9 p.Arg407Ter Pathogenic ★ same condition
ALG9 p.Cys71Ter Likely pathogenic ★ same condition
ALG9 p.Gly512Ter Pathogenic ★ same condition
ALG9 p.Ser388fs 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/alg9-p-ala175fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown