Is AHI1 p.Pro560fs (c.1677dup) pathogenic?

AHI1 p.Pro560fs (c.1677dup) is classified Pathogenic in AHI1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-13). Absent from gnomAD; Associated with Joubert syndrome.

What condition is associated with AHI1 p.Pro560fs (c.1677dup)?

AHI1 p.Pro560fs (c.1677dup) is associated with Joubert syndrome (ClinVar).

How common is AHI1 p.Pro560fs (c.1677dup) in the general population?

AHI1 p.Pro560fs (c.1677dup) is absent from gnomAD (gnomAD).

AHI1 p.Pro560fs

c.1677dup · rs1554350503 · VCV461742

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Joubert 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 13 of 29
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.5	GERP 0.47, 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: AHI1
Protein: p.Pro560fs
Coding: c.1677dup
MANE Select: NM_001134831
dbSNP: rs1554350503
Type: Duplication
Location: chr6:135447109 (GRCh38)
Gene constraint: LOEUF 1.069 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 62.03 · 1 PDB

Full AHI1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Joubert syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AHI1 p.Pro560Ala Uncertain significance ★★ ⚠ same residue
AHI1 p.Pro560= Conflicting classifications of pathogenicity ★ same residue
AHI1 p.Arg235fs Pathogenic/Likely pathogenic ★★ same condition
AHI1 p.Asn1020fs Pathogenic/Likely pathogenic ★★ same condition
AHI1 p.Cys614fs Pathogenic/Likely pathogenic ★★ same condition
AHI1 p.Leu33fs Pathogenic/Likely pathogenic ★★ same condition
AHI1 p.Leu37fs Pathogenic/Likely pathogenic ★★ same condition
AHI1 p.Leu413fs 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/ahi1-p-pro560fs (accessed [today's date]).

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