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Variant: NM_000261.2:c.761C>G

CA343726243

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: 653c89c3-854b-4091-af70-2528414120a3
Approved on: 2022-12-14
Published on: 2022-12-14

HGVS expressions

NM_000261.2:c.761C>G
NC_000001.11:g.171636679G>C
CM000663.2:g.171636679G>C
NC_000001.10:g.171605819G>C
CM000663.1:g.171605819G>C
NC_000001.9:g.169872442G>C
NG_008859.1:g.20955C>G
ENST00000037502.11:c.761C>G
ENST00000637303.1:c.235-1951G>C
ENST00000638471.1:c.*99C>G
ENST00000037502.10:c.761C>G
ENST00000614688.1:c.761C>G
NM_000261.1:c.761C>G

Uncertain Significance

Met criteria codes 3
PM5_Supporting PP3 PM2_Supporting
Not Met criteria codes 12
BS3 BS1 PS2 PS3 PS4 PS1 BP7 BP4 BA1 PP1 PM4 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Glaucoma VCEP
The c.761C>G variant in MYOC is a missense variant predicted to cause substitution of Proline by Arginine at amino acid 254 (p.Pro254Arg). 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 = 0.924, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function. There was no functional evidence predicting a damaging or benign impact of this variant on MYOC function. Only 1 segregation had been reported for juvenile open angle glaucoma (JOAG) (PMID: 26095806), not meeting the ≥ 3 segregations required for PP1. Only 1 proband with JOAG had been reported (PMID: 26095806), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting. Another missense variant (c.761C>T, p.Pro254Leu, Grantham score = 98, ClinVar ID: 1342967) in the same codon has been classified as likely pathogenic for JOAG by the ClinGen Glaucoma VCEP. The c.761C>G, p.Pro254Arg variant has a higher Grantham score (= 103) 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 3 and to be classified as a variant of uncertain significance (uncertain significance classification range -1 to 5) for juvenile open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v1, 12 Oct 2021): PP3, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM5_Supporting
Another missense variant (c.761C>T, p.Pro254Leu, Grantham score = 98, ClinVar ID: 1342967) in the same codon has been classified as likely pathogenic for juvenile open angle glaucoma by the ClinGen Glaucoma VCEP. The c.761C>G, p.Pro254Arg variant has a higher Grantham score (= 103) 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.
PP3
The REVEL score = 0.924, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function.
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.
Not Met criteria codes
BS3
No functional evidence has been found for this variant.
BS1
This criterion was not met as PM2_Supporting has been met.
PS2
This variant has not been identified de novo.
PS3
No functional evidence has been found for this variant.
PS4
Only 1 proband with JOAG had been reported (PMID: 26095806), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting.
PS1
An established pathogenic variant causing this same amino acid change has not been identified.
BP7
This is not a synonymous or non-coding variant.
BP4
This criterion was not met as PP3 has been met.
BA1
This criterion was not met as PM2_Supporting has been met.
PP1
Only 1 segregation had been reported for juvenile open angle glaucoma (PMID: 26095806), not meeting the ≥ 3 segregations required for PP1.
PM4
This variant does not cause a protein length change.
PM6
This variant has not been identified de novo.
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