Is AHI1 p.Arg386= (c.1156C>A) pathogenic?

AHI1 p.Arg386= (c.1156C>A) is classified Likely benign in AHI1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-27). Very rare (popmax 0.00177%, sas); Associated with Joubert syndrome.

What condition is associated with AHI1 p.Arg386= (c.1156C>A)?

AHI1 p.Arg386= (c.1156C>A) is associated with Joubert syndrome (ClinVar).

How common is AHI1 p.Arg386= (c.1156C>A) in the general population?

AHI1 p.Arg386= (c.1156C>A) is very rare (popmax 0.00177%, sas) (gnomAD).

AHI1 p.Arg386=

c.1156C>A · rs183862577 · VCV2807079

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00177%, sas)

Conditions

Joubert syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.7	GERP 1.2, phastCons 1
Overall
CADD	4.345	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00177% South Asian · 1/56,604 alleles

Filtering AF 0.000268% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000172%

Overall 0.000555% 8/1,440,652 alleles · very rare exomes 8/1,288,566 · genomes 0/152,086 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00177%	56,604
European (non-Finnish)	0.000645%	155,095

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.Arg386=
Coding: c.1156C>A
MANE Select: NM_001134831
dbSNP: rs183862577
Type: single nucleotide variant
Location: chr6:135455922 (GRCh38)
Gene constraint: LOEUF 1.069 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 62.03 · 1 PDB
Residue 386: the 'interaction with hap1' region

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.Arg386Trp Uncertain significance ★★ ⚠ same residue
AHI1 p.Arg386Gln Conflicting classifications of pathogenicity ★ ⚠ 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-arg386 (accessed [today's date]).

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