The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000261.2:c.1496T>G

CA343722837

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: a215a4e6-5a7d-4bee-9d62-6a854b218b95
Approved on: 2022-05-10
Published on: 2022-05-25

HGVS expressions

NM_000261.2:c.1496T>G
NC_000001.11:g.171635944A>C
CM000663.2:g.171635944A>C
NC_000001.10:g.171605084A>C
CM000663.1:g.171605084A>C
NC_000001.9:g.169871707A>C
NG_008859.1:g.21690T>G
ENST00000037502.11:c.1496T>G
ENST00000637303.1:c.235-2686A>C
ENST00000638471.1:c.*834T>G
ENST00000037502.10:c.1496T>G
ENST00000614688.1:c.*460T>G
NM_000261.1:c.1496T>G
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Uncertain Significance

Met criteria codes 4
PP3 PS3_Supporting PM2_Supporting PM5_Supporting
Not Met criteria codes 11
PP1 PM4 PM6 BA1 BS3 BS1 BP4 BP7 PS2 PS4 PS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Glaucoma VCEP
The c.1496T>G variant in MYOC is a missense variant predicted to cause substitution of Isoleucine by Serine at amino acid 499 (p.Ile499Ser). 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 = 0.798, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function. A previous study (PMID: 11004290) demonstrated that the Ile499Ser protein had increased insolubility levels compared to wild type myocilin protein and met the OddsPath threshold for PS3_Supporting (> 2.1), indicating that this variant did impact protein function. Only 1 segregation had been reported for juvenile open angle glaucoma (JOAG) (PMID: 11004290), not meeting the ≥ 3 segregations required for PP1. Only 1 proband with JOAG had been reported (PMID: 11004290), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting. Another missense variant (c.1495A>T, p.Ile499Phe, Grantham score = 21, PMID: 9328473) in the same codon has been classified as likely pathogenic for JOAG by the ClinGen Glaucoma VCEP. The c.1496T>G, p.Ile499Ser variant has a higher Grantham score (= 142) 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 4 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, PS3_Supporting, PM2_Supporting, PM5_Supporting
Met criteria codes
PP3
The REVEL score = 0.798, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function.
PS3_Supporting
A previous study (PMID: 11004290) demonstrated that the Ile499Ser protein had increased insolubility levels compared to wild type myocilin protein and met the OddsPath threshold for PS3_Supporting (> 2.1), indicating that this variant did impact protein 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.
PM5_Supporting
Another missense variant (c.1495A>T, p.Ile499Phe, Grantham score = 21, PMID: 9328473) in the same codon has been classified as likely pathogenic for juvenile open angle glaucoma by the ClinGen Glaucoma VCEP. The c.1496T>G, p.Ile499Ser variant has a higher Grantham score (= 142) 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.
Not Met criteria codes
PP1
Only 1 segregation had been reported for juvenile open angle glaucoma (PMID: 11004290), 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.
BA1
This criterion was not met as PM2_Supporting has been met.
BS3
This criterion was not met as PS3_Supporting has been met.
BS1
This criterion was not met as PM2_Supporting has been met.
BP4
This criterion was not met as PP3 has been met.
BP7
This is not a synonymous or non-coding variant.
PS2
This variant has not been identified de novo.
PS4
Only 1 proband with JOAG had been reported (PMID: 11004290), 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.
Curation History
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