Is AHI1 p.Pro501= (c.1503A>G) pathogenic?

AHI1 p.Pro501= (c.1503A>G) is classified Likely benign in AHI1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-24). Absent from gnomAD v4.1; Associated with Joubert syndrome.

What condition is associated with AHI1 p.Pro501= (c.1503A>G)?

AHI1 p.Pro501= (c.1503A>G) is associated with Joubert syndrome (ClinVar).

How common is AHI1 p.Pro501= (c.1503A>G) in the general population?

AHI1 p.Pro501= (c.1503A>G) is absent from gnomAD v4.1 (gnomAD).

AHI1 p.Pro501=

c.1503A>G · rs2484788896 · VCV2786786

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,594,114)

Conditions

Joubert syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.065	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.48	GERP 0.32, phastCons 1
Overall
CADD	9.876	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,594,114). 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.Pro501=
Coding: c.1503A>G
MANE Select: NM_001134831
dbSNP: rs2484788896
Type: single nucleotide variant
Location: chr6:135448413 (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.Pro501Leu Uncertain significance ★★ ⚠ same residue
AHI1 p.Pro501Ala Uncertain significance ★ 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.2623+1G>A 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-pro501 (accessed [today's date]).

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