Is UBIAD1 p.Arg124= (c.370C>A) pathogenic?

UBIAD1 p.Arg124= (c.370C>A) is classified Benign in UBIAD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Ultra-rare (popmax 0.03%, amr); Associated with Schnyder corneal dystrophy.

What condition is associated with UBIAD1 p.Arg124= (c.370C>A)?

UBIAD1 p.Arg124= (c.370C>A) is associated with Schnyder corneal dystrophy (ClinVar).

How common is UBIAD1 p.Arg124= (c.370C>A) in the general population?

UBIAD1 p.Arg124= (c.370C>A) is ultra-rare (popmax 0.03%, amr) (gnomAD).

How is Schnyder corneal dystrophy inherited?

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

UBIAD1 p.Arg124=

c.370C>A · rs748615089 · VCV291823

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.03%, amr)

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 2.2	GERP 0.53, phastCons 1
Overall
CADD	11.83	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.03% Admixed American · 18/60,004 alleles

Filtering AF 0.0194% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.016%

Overall 0.00409% 66/1,614,038 alleles · ultra-rare exomes 59/1,461,884 · genomes 7/152,154 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.03%	3,334
Ashkenazi Jewishnot grpmax-eligible	0.0135%	7,402
Remaining individualsnot grpmax-eligible	0.0064%	15,622
European (non-Finnish)	0.00339%	29,501

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
Protein: p.Arg124=
Coding: c.370C>A
MANE Select: NM_013319
dbSNP: rs748615089
Type: single nucleotide variant
Location: chr1:11273901 (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-p-arg124 (accessed [today's date]).

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