Is AHI1 p.Val902= (c.2706T>C) pathogenic?

AHI1 p.Val902= (c.2706T>C) is classified Likely benign in AHI1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-04). Ultra-rare (popmax 0.0902%, sas); Associated with Joubert syndrome.

What condition is associated with AHI1 p.Val902= (c.2706T>C)?

AHI1 p.Val902= (c.2706T>C) is associated with Joubert syndrome (ClinVar).

How common is AHI1 p.Val902= (c.2706T>C) in the general population?

AHI1 p.Val902= (c.2706T>C) is ultra-rare (popmax 0.0902%, sas) (gnomAD).

AHI1 p.Val902=

c.2706T>C · rs576859418 · VCV1102959

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0902%, sas)

Conditions

Joubert syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.152	moderately benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.3	GERP -0.67, phastCons 1
Overall
CADD	8.077	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0902% South Asian · 82/90,876 alleles

Filtering AF 0.0744% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0686%

Overall 0.00639% 103/1,610,868 alleles · ultra-rare exomes 99/1,459,076 · genomes 4/151,792 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0902%	1,108
Middle Eastern	0.0165%	6,046
Remaining individualsnot grpmax-eligible	0.00802%	12,470
European (non-Finnish)	0.00127%	78,527

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.Val902=
Coding: c.2706T>C
MANE Select: NM_001134831
dbSNP: rs576859418
Type: single nucleotide variant
Location: chr6:135427225 (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 902: a UniProt-annotated variant site (in jbts3)

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.Val902Asp 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
AHI1 c.2623+1G>T 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-val902 (accessed [today's date]).

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