Is PAX6 p.Ser367= (c.1101A>G) pathogenic?

PAX6 p.Ser367= (c.1101A>G) is classified Likely benign in PAX6 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-05). Very rare (popmax 0.0011%, sas); Associated with aniridia 1.

What condition is associated with PAX6 p.Ser367= (c.1101A>G)?

PAX6 p.Ser367= (c.1101A>G) is associated with aniridia 1, Peters anomaly (ClinVar).

How common is PAX6 p.Ser367= (c.1101A>G) in the general population?

PAX6 p.Ser367= (c.1101A>G) is very rare (popmax 0.0011%, sas) (gnomAD).

PAX6 p.Ser367=

c.1101A>G · rs1328757289 · VCV1157674

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

aniridia 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.6	GERP -4.2
Overall
CADD	3.337	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,072 alleles

Overall 6.2e-05% 1/1,614,060 alleles · very rare exomes 1/1,461,856 · genomes 0/152,204 · joint denominator

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: PAX6
Protein: p.Ser367=
Coding: c.1101A>G
MANE Select: NM_001368894
dbSNP: rs1328757289
Type: single nucleotide variant
Location: chr11:31790834 (GRCh38)
Gene constraint: LOEUF 0.226 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.35 · 2 PDB
Residue 367: the 'required for suppression of nfatc1-mediated transcription' region

Full PAX6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

aniridia 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Peters anomaly

Similar variants

PAX6 p.Ser367Ter Pathogenic same residue
PAX6 c.1074+1G>C Pathogenic ★★ same condition
PAX6 c.1075-2A>G Pathogenic ★★ same condition
PAX6 c.1225+5G>A Pathogenic/Likely pathogenic ★★ same condition
PAX6 c.141+1G>A Pathogenic ★★ same condition
PAX6 c.399+1G>A Pathogenic ★★ same condition
PAX6 c.399+1G>C Pathogenic ★★ same condition
PAX6 c.958+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/pax6-p-ser367 (accessed [today's date]).

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