Is AHI1 p.Pro560= (c.1680A>G) pathogenic?

AHI1 p.Pro560= (c.1680A>G) is classified Conflicting classifications of pathogenicity in AHI1 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-26). Rare (popmax 0.237%, eas); Associated with Joubert syndrome 3.

What condition is associated with AHI1 p.Pro560= (c.1680A>G)?

AHI1 p.Pro560= (c.1680A>G) is associated with Joubert syndrome 3, Joubert syndrome (ClinVar).

How common is AHI1 p.Pro560= (c.1680A>G) in the general population?

AHI1 p.Pro560= (c.1680A>G) is rare (popmax 0.237%, eas) (gnomAD).

AHI1 p.Pro560=

c.1680A>G · rs200949030 · VCV355507

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.237%, eas)

Conditions

Joubert syndrome 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.015	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1	GERP -5.5
Overall
CADD	11.95	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.237% East Asian · 104/43,814 alleles

Filtering AF 0.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.187%

Overall 0.00762% 122/1,600,990 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.237%	421
Remaining individualsnot grpmax-eligible	0.0178%	5,606
South Asian	0.00444%	22,530
European (non-Finnish)	0.000256%	390,755

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: AHI1
Protein: p.Pro560=
Coding: c.1680A>G
MANE Select: NM_001134831
dbSNP: rs200949030
Type: single nucleotide variant
Location: chr6:135447107 (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 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Joubert syndrome

Similar variants

AHI1 p.Pro560Ala Uncertain significance ★★ ⚠ same residue
AHI1 p.Pro560fs Pathogenic ★ same residue
AHI1 c.1152-1G>A Pathogenic/Likely pathogenic ★★ same condition
AHI1 c.1152-2A>G Pathogenic ★★ same condition
AHI1 c.1626+1G>A Pathogenic/Likely pathogenic ★★ same condition
AHI1 c.1779+1G>T Pathogenic/Likely pathogenic ★★ same condition
AHI1 c.2492+1G>A Pathogenic/Likely pathogenic ★★ same condition
AHI1 c.2493-2A>G 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/ahi1-p-pro560 (accessed [today's date]).

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