Is UBIAD1 c.*467G>A pathogenic?

UBIAD1 c.467G>A is classified Benign in UBIAD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Rare (popmax 0.68%, afr); Associated with Schnyder corneal dystrophy.

What condition is associated with UBIAD1 c.*467G>A?

UBIAD1 c.*467G>A is associated with Schnyder corneal dystrophy (ClinVar).

How common is UBIAD1 c.*467G>A in the general population?

UBIAD1 c.*467G>A is rare (popmax 0.68%, afr) (gnomAD).

How is Schnyder corneal dystrophy inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

UBIAD1 c.*467G>A

rs112285480 · VCV876001

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.68%, afr)

Conditions

Schnyder corneal dystrophy

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 1.7	GERP -0.53, phastCons 0.007
Non-coding constraint	Z 1.36	1 kb window · o/e 0.90 · regional · uncalibrated
Overall
CADD	6.916	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.68% African / African-American · 292/42,914 alleles

Filtering AF 0.616% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.591%

Overall 0.147% 327/222,404 alleles · rare exomes 8/70,180 · genomes 319/152,224 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.68%	147
Admixed American	0.158%	633
Remaining individualsnot grpmax-eligible	0.0907%	1,102

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: UBIAD1
Coding: c.*467G>A
MANE Select: NM_013319
dbSNP: rs112285480
Type: single nucleotide variant
Location: chr1:11286598 (GRCh38)
Gene constraint: LOEUF 0.92 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.21

Full UBIAD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Schnyder corneal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Schnyder corneal dystrophy (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages

Similar variants

UBIAD1 p.Gly177Glu Pathogenic/Likely pathogenic ★★ same condition
UBIAD1 p.Leu251Ile Uncertain significance ★★ ⚠ same condition
UBIAD1 p.Pro64Leu Uncertain significance ★★ ⚠ same condition
UBIAD1 c.-47T>G Benign ★★ same condition
UBIAD1 c.*1060G>A Benign ★★ same condition
UBIAD1 c.*1304C>T Benign ★★ same condition
UBIAD1 c.*148A>G Benign ★★ same condition
UBIAD1 c.*904T>C Benign ★★ 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/ubiad1-c-star-467g-a (accessed [today's date]).

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