The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000261.2:c.1139A>C

CA343724571

1342203 (ClinVar)

Gene: MYOC (HGNC:4653)
Condition: open-angle glaucoma (MONDO:0005338)
Inheritance Mode: Autosomal dominant inheritance
UUID: 9c3b9acb-015c-45ad-956e-7b10bbf078bd
Approved on: 2026-01-13
Published on: 2026-01-12

HGVS expressions

NM_000261.2:c.1139A>C
NC_000001.11:g.171636301T>G
CM000663.2:g.171636301T>G
NC_000001.10:g.171605441T>G
CM000663.1:g.171605441T>G
NC_000001.9:g.169872064T>G
NG_008859.1:g.21333A>C
ENST00000037502.11:c.1139A>C
ENST00000637303.1:c.235-2329T>G
ENST00000638471.1:c.*477A>C
ENST00000037502.10:c.1139A>C
ENST00000614688.1:c.*103A>C
NM_000261.1:c.1139A>C
More

Pathogenic

Met criteria codes 6
PS4_Moderate PS3_Moderate PP3_Strong PP1_Strong PM5 PM2_Supporting
Not Met criteria codes 8
BA1 BS1 BS3 BP4 BP7 PS1 PS2 PM4

Evidence Links 9

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Glaucoma Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MYOC Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Glaucoma VCEP
The c.1139A>C variant in MYOC is a missense variant predicted to cause substitution of Aspartic Acid by Alanine at amino acid 380 (p.Asp380Ala). The highest minor allele frequency of this variant was in the European (non-Finnish) genetic ancestry group of gnomAD (v4.1.0) = 0.00000085 (1 allele out of 1,179,992), which met the ≤ 0.0001 threshold set for PM2_Supporting in a genetic ancestry group of at least 10,000 alleles. The REVEL score = 0.97, which met the ≥ 0.932 threshold for PP3_Strong, predicting a damaging effect on MYOC function. The Asp380Ala protein had increased insolubility, instability and reduced secretion levels compared to wild type myocilin protein in these studies (PMIDs: 20334347, 21612213, 23129764, 16466712). The assays met the OddsPath threshold for PS3_Moderate (> 4.3), indicating that this variant did impact protein function. This protein has also been assessed in these other studies (PMIDs: 15069026, 24333014), however, the same level of evidence was not met. 31 segregations in 6 families, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMIDs: 17893668, 9863594, 9832047), which fulfilled PP1_Strong (≥ 7 meioses in > 1 family). 7 probands with JOAG or POAG have been reported carrying this variant (PMIDs: 17893668, 9863594, 9832047), which met PS4_Moderate (≥ 6 probands). Two other missense variants (c.1138G>C, p.Asp380His, Grantham score = 81, ClinVar ID: 7961 and c.1139A>G, p.Asp380Gly Grantham score = 94, ClinVar ID: 1342964) in the same codon have been classified as likely pathogenic for juvenile open angle glaucoma by the ClinGen Glaucoma VCEP. The c.1139A>C, p.Asp380Ala variant has a higher Grantham score (= 126) than the previously classified amino acid changes, was not predicted to affect splicing as assessed with SpliceAI (≤ 0.2), and met PP3, meeting the conditions for PM5 to apply. In summary, this variant met the criteria to receive a score of 14 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): PP1_Strong, PP3_Strong, PS3_Moderate, PS4_Moderate, PM5, PM2_Supporting (PP3 and PM5 capped at 5 points).
Met criteria codes
PS4_Moderate
7 probands with JOAG or POAG have been reported carrying this variant (PMIDs: 17893668, 9863594, 9832047), which met PS4_Moderate (≥ 6 probands).
PS3_Moderate
The Asp380Ala protein had increased insolubility, instability and reduced secretion levels compared to wild type myocilin protein in these studies (PMIDs: 20334347, 21612213, 23129764, 16466712). The assays met the OddsPath threshold for PS3_Moderate (> 4.3), indicating that this variant did impact protein function. This protein has also been assessed in these other studies (PMIDs: 15069026, 24333014), however, the same level of evidence was not met.

PP3_Strong
The REVEL score = 0.97, which met the ≥ 0.932 threshold for PP3_Strong, predicting a damaging effect on MYOC function.
PP1_Strong
31 segregations in 6 families, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMIDs: 17893668, 9863594, 9832047), which fulfilled PP1_Strong (≥ 7 meioses in > 1 family).
PM5
Two other missense variants (c.1138G>C, p.Asp380His, Grantham score = 81, ClinVar ID: 7961 and c.1139A>G, p.Asp380Gly Grantham score = 94, ClinVar ID: 1342964) in the same codon have been classified as likely pathogenic for juvenile open angle glaucoma by the ClinGen Glaucoma VCEP. The c.1139A>C, p.Asp380Ala variant has a higher Grantham score (= 126) than the previously classified amino acid changes, was not predicted to affect splicing as assessed with SpliceAI (≤ 0.2), and met PP3, meeting the conditions for PM5 to apply. This variant would still be classified as pathogenic without the use of PM5 and was used to apply PM5 to variant MYOC c.1138G>T, p.Asp380Tyr which is located at the same amino acid residue.
PM2_Supporting
The highest minor allele frequency of this variant was in the European (non-Finnish) genetic ancestry group of gnomAD (v4.1.0) = 0.0000008 (1 allele out of 1,179,992), which met the ≤ 0.0001 threshold set for PM2_Supporting in a genetic ancestry group of at least 10,000 alleles.
Not Met criteria codes
BA1
This criterion was not met as PM2_Supporting has been met.
BS1
This criterion was not met as PM2_Supporting has been met.
BS3
This criterion was not met as PS3_Moderate has been met.
BP4
This criterion was not met as PP3 has been met.
BP7
This is not an intronic, synonymous or non-coding variant.
PS1
An established LP or P variant causing this same amino acid change has not been identified.
PS2
This variant has not been identified de novo.
PM4
This variant does not cause a protein length change.
Curation History
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