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MYOC p.Ser341Pro

c.1021T>C · rs1572210748 · VCV1439558

Pathogenic Expert panel
Classification
Pathogenic
ClinVar
Review
Expert panel ★★★☆
ClinVar · 2 submitters
AlphaMissense
likely pathogenic
0.8693 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
3/3 damaging
AlphaMissense, REVEL, SaProt
Conditions
1
open-angle glaucoma

ClinGen expert panel — Glaucoma VCEP

Pathogenic for open-angle glaucoma. Applied ACMG criteria (verbatim):

PP1_Strong PP3_Moderate PM2_Supporting PS3 PS4_Moderate

Curation rationale (ClinGen, verbatim)

The c.1021T>C variant in MYOC is a missense variant predicted to cause substitution of Serine by Proline at amino acid 341 (p.Ser341Pro). This variant was not found in any genetic ancestry group of gnomAD (v4.1.0), meeting the ≤ 0.0001 threshold set for PM2_Supporting in a genetic ancestry group of at least 10,000 alleles. The REVEL score = 0.821, which was within the 0.773-0.931 range for PP3_Moderate, predicting a damaging effect on MYOC function. A transgenic mouse model carrying human MYOC Ser341Pro (PMID: 38212635), and displaying reduced secretion of the Ser341Pro protein in vivo, exhibited a glaucoma phenotype (including IOP elevation and retina ganglion cell loss), meeting PS3. 12 segregations in 4 families, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMIDs: 17867509, 24825108, 33214997, 25777973), which fulfilled PP1_Strong (≥7 meioses in >1 family). There were more family studies published than presented here. 8 probands with JOAG or POAG have been reported carrying this variant (PMIDs: 9510647, 24825108, 25777973, 33214997, 17867509, ClinVar: Invitae), which met PS4_Moderate (≥ 6 probands). In summary, this variant met the criteria to receive a score of 13 and to be classified as pathogenic (pathogenic classification ≥ 10, adapted from PMID: 32720330) for juvenile open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v2.0.0, 5 Dec 2024): PS3, PP1_Strong, PS4_Moderate, PP3_Moderate, PM2_Supporting

ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.

Computational evidence

Protein change
AlphaMissense0.8693likely pathogenic ✓ concordant with ClinVar · top 5% in MYOC
REVEL0.821moderately pathogenic-leaning
SaProtLLR -12.16damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI—not assessed · no allele here is in the release
Constraint at this position
ConservationphyloP 5.9phastCons 1
Regional constrainto/e 0.92unconstrained · MANE · 17 kb · p 0.038 · regional, not allelic
Overall
CADD21.3PHRED · 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
MYOC
Protein
p.Ser341Pro
Coding
c.1021T>C
MANE Select
NM_000261
dbSNP
rs1572210748
Type
single nucleotide variant
Location
chr1:171636419 (GRCh38)
Gene constraint
LOEUF 1.343 · pLI <0.01 (gnomAD)
Structure
AlphaFold pLDDT 79.40 · 24 PDB
Residue 341
a β-strand; the olfactomedin-like domain; a UniProt-annotated variant site (in glc1a)
Full MYOC gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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/myoc-p-ser341pro (accessed [today's date]).

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