Is KRT12 p.Tyr429Asp (c.1285T>G) pathogenic?

KRT12 p.Tyr429Asp (c.1285T>G) is classified Pathogenic in KRT12 (ClinVar, No assertion criteria, 2 submitters; last evaluated 1997-12-01). AlphaMissense: likely pathogenic (0.9045); Absent from gnomAD v4.1; Associated with corneal dystrophy, Meesmann, 1.

What condition is associated with KRT12 p.Tyr429Asp (c.1285T>G)?

KRT12 p.Tyr429Asp (c.1285T>G) is associated with corneal dystrophy, Meesmann, 1 (ClinVar).

How common is KRT12 p.Tyr429Asp (c.1285T>G) in the general population?

KRT12 p.Tyr429Asp (c.1285T>G) is absent from gnomAD v4.1 (gnomAD).

How is Meesmann corneal dystrophy inherited?

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

What do computational predictors say about KRT12 p.Tyr429Asp (c.1285T>G)?

AlphaMissense predicts likely pathogenic (score 0.9045) — an in-silico prediction, not a clinical call.

KRT12 p.Tyr429Asp

c.1285T>G · rs58162394 · VCV7925

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9045 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

corneal dystrophy, Meesmann, 1

Computational evidence

Protein change
AlphaMissense	0.9045	likely pathogenic ✓ concordant with ClinVar · top 3% in KRT12
REVEL	0.99	strongly pathogenic-leaning
SaProt	LLR -12.52	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 9	GERP 2, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 5,522 bp · p 0.13 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: KRT12
Protein: p.Tyr429Asp
Coding: c.1285T>G
MANE Select: NM_000223
dbSNP: rs58162394
Type: single nucleotide variant
Location: chr17:40863154 (GRCh38)
Gene constraint: LOEUF 0.979 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.57
Residue 429: the if rod domain; a UniProt-annotated variant site (in mecd1); the 'coil 2' region

Full KRT12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For Meesmann corneal dystrophy (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood

Similar variants

KRT12 p.Pro15Ser Benign ★★ same condition
KRT12 p.Met129Thr Pathogenic ★ same condition
KRT12 p.Arg187Gly Uncertain significance ★ ⚠ same condition
KRT12 p.Asp175Asn Conflicting classifications of pathogenicity ★ ⚠ same condition
KRT12 p.Glu330Ter Uncertain significance ★ same condition
KRT12 p.Leu384Pro Uncertain significance ★ ⚠ same condition
KRT12 p.Leu394Pro Conflicting classifications of pathogenicity ★ ⚠ same condition
KRT12 p.Arg135Gly 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/krt12-p-tyr429asp (accessed [today's date]).

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