The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • ClinVar Id was derived from the Allele Registry.


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

CA343724571

1342203 (ClinVar)

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: 9c3b9acb-015c-45ad-956e-7b10bbf078bd
Approved on: 2022-02-21
Published on: 2022-07-11

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
NM_000261.2(MYOC):c.1139A>C (p.Asp380Ala)

Pathogenic

Met criteria codes 6
PM5_Supporting PS3_Moderate PP1_Strong PS4_Moderate PM2_Supporting PP3
Not Met criteria codes 9
BS3 BS1 BP7 BP4 PS2 PS1 BA1 PM4 PM6

Evidence Links 4

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Glaucoma Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.1

PDF
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). This variant was not found in any population of gnomAD (v2.1.1), meeting the ≤ 0.0001 threshold set for PM2_Supporting in a population of at least 10,000 alleles. The REVEL score = 0.97, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function. A previous study (PMID: 16466712) demonstrated that the Asp380Ala protein had reduced secretion levels compared to wild type myocilin protein and met the OddsPath threshold for PS3_Moderate (> 4.3), indicating that this variant did impact protein function. 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). Another missense variant (c.1138G>C, p.Asp380His, Grantham score = 81, ClinVar ID: 7961) in the same codon has 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 change, was not predicted to affect splicing as assessed with SpliceAI (≤ 0.2), and met PP3, meeting the conditions for PM5_Supporting to apply. In summary, this variant met the criteria to receive a score of 11 and to be classified as pathogenic (pathogenic classification ≥ 10) for juvenile open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v1, 12 Oct 2021): PP1_Strong, PS3_Moderate, PS4_Moderate, PP3, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM5_Supporting
Another missense variant (c.1138G>C, p.Asp380His, Grantham score = 81, ClinVar ID: 7961) in the same codon has 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 change, was not predicted to affect splicing as assessed with SpliceAI (≤ 0.2), and met PP3, meeting the conditions for PM5_Supporting to apply. This variant would still be classified as pathogenic without the use of PM5_Supporting and was used to apply PM5 to variant MYOC c.1138G>T, p.Asp380Tyr which is located at the same amino acid residue.
PS3_Moderate
A previous study (PMID: 16466712) demonstrated that the Asp380Ala protein had reduced secretion levels compared to wild type myocilin protein and met the OddsPath threshold for PS3_Moderate (> 4.3), indicating that this variant did impact protein 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).
PS4_Moderate
7 probands with JOAG or POAG have been reported carrying this variant (PMIDs: 17893668, 9863594, 9832047), which met PS4_Moderate (≥ 6 probands).
PM2_Supporting
This variant was not found in any population of gnomAD (v2.1.1), meeting the ≤ 0.0001 threshold set for PM2_Supporting in a population of at least 10,000 alleles.
PP3
The REVEL score = 0.97, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function.
Not Met criteria codes
BS3
This criterion was not met as PS3_Moderate has been met.
BS1
This criterion was not met as PM2_Supporting has been met.
BP7
This is not a synonymous or non-coding variant.
BP4
This criterion was not met as PP3 has been met.
PS2
This variant has not been identified de novo.
PS1
An established pathogenic variant causing this same amino acid change has not been identified.
BA1
This criterion was not met as PM2_Supporting has been met.
PM4
This variant does not cause a protein length change.
PM6
This variant has not been identified de novo.
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