Is AHI1 p.Arg830= (c.2490G>A) pathogenic?

AHI1 p.Arg830= (c.2490G>A) is classified Benign/Likely benign in AHI1 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-06-01). Rare (popmax 0.502%, afr); Associated with Joubert syndrome.

What condition is associated with AHI1 p.Arg830= (c.2490G>A)?

AHI1 p.Arg830= (c.2490G>A) is associated with Joubert syndrome (ClinVar).

How common is AHI1 p.Arg830= (c.2490G>A) in the general population?

AHI1 p.Arg830= (c.2490G>A) is rare (popmax 0.502%, afr) (gnomAD).

AHI1 p.Arg830=

c.2490G>A · rs368942099 · VCV260847

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.502%, afr)

Conditions

Joubert syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.136	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.14	GERP -3.2, phastCons 0.98
Overall
CADD	6.646	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.502% African / African-American · 368/73,240 alleles

Filtering AF 0.46% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.443%

Overall 0.0278% 422/1,519,080 alleles · rare exomes 194/1,367,236 · genomes 228/151,844 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.502%	199
Admixed American	0.0415%	2,410
Remaining individualsnot grpmax-eligible	0.0354%	2,824
Middle Eastern	0.017%	5,866
South Asian	0.0012%	83,374
European (non-Finnish)	0.000723%	138,377

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.Arg830=
Coding: c.2490G>A
MANE Select: NM_001134831
dbSNP: rs368942099
Type: single nucleotide variant
Location: chr6:135429884 (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 830: a UniProt-annotated variant site (in jbts3); a UniProt-annotated variant site (in)

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.Arg830Gln Uncertain significance ★★ ⚠ same residue
AHI1 p.Arg830Trp Benign/Likely benign ★★ 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-arg830 (accessed [today's date]).

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