MYOC p.Ser341Pro
c.1021T>C · rs1572210748 · VCV1439558
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 | ||
| AlphaMissense | 0.8693 | likely pathogenic ✓ concordant with ClinVar · top 5% in MYOC |
|---|---|---|
| REVEL | 0.821 | moderately pathogenic-leaning |
| SaProt | LLR -12.16 | damaging |
| ⇒ AlphaMissense, REVEL and SaProt all call this damaging. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | phastCons 1 |
| Regional constraint | o/e 0.92 | unconstrained · MANE · 17 kb · p 0.038 · regional, not allelic |
| Overall | ||
| CADD | 21.3 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
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)
Similar variants
- MYOC p.Ala363Thr Likely pathogenic ★★★ same condition
- MYOC p.Arg272Gly Likely pathogenic ★★★ same condition
- MYOC p.Asn450Tyr Likely pathogenic ★★★ same condition
- MYOC p.Asn480Lys Pathogenic ★★★ same condition
- MYOC p.Asp380Ala Pathogenic ★★★ same condition
- MYOC p.Asp380Gly Likely pathogenic ★★★ same condition
- MYOC p.Asp380His Likely pathogenic ★★★ same condition
- MYOC p.Asp380Tyr Likely 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/myoc-p-ser341pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown