Evidence Repository
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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CA1244109

Gene: MYOC
Condition: primary open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 82d818dc-ceb5-46e0-a89b-d1175498efcb

HGVS expressions

NM_000261.2:c.974C>T
NC_000001.11:g.171636466G>A
CM000663.2:g.171636466G>A
NC_000001.10:g.171605606G>A
CM000663.1:g.171605606G>A
NC_000001.9:g.169872229G>A
NG_008859.1:g.21168C>T
ENST00000037502.11:c.974C>T
ENST00000637303.1:c.235-2164G>A
ENST00000638471.1:c.*312C>T
ENST00000037502.10:c.974C>T
ENST00000614688.1:c.974C>T
NM_000261.1:c.974C>T

Uncertain Significance

Met criteria codes 2
PM2_Supporting PP3
Not Met criteria codes 13
BA1 BS3 BS1 BP7 BP4 PS2 PS1 PS3 PS4 PP1 PM5 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.974C>T variant in MYOC is a missense variant predicted to cause substitution of Threonine by Methionine at amino acid 325 (p.Thr325Met). The highest minor allele frequency of this variant was in the South Asian population of gnomAD (v2.1.1) = 0.00006536 (2 alleles out of 30,602), which met the ≤ 0.0001 threshold set for PM2_Supporting in a population of at least 10,000 alleles. The REVEL score = 0.777, 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 proband with primary open angle glaucoma had been reported (PMID: 24825108), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting. In summary, this variant met the criteria to receive a score of 2 and to be classified as a variant of uncertain significance (uncertain significance classification range -1 to 5) for primary open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v1, 12 Oct 2021): PP3, PM2_Supporting.
Met criteria codes
PM2_Supporting
The highest minor allele frequency of this variant was in the South Asian population of gnomAD (v2.1.1) = 0.00006536 (2 alleles out of 30,602), which met the ≤ 0.0001 threshold set for PM2_Supporting in a population of at least 10,000 alleles.
PP3
The REVEL score = 0.777, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function.
Not Met criteria codes
BA1
This criterion was not met as PM2_Supporting has been met.
BS3
No functional evidence has been found for this variant.
BS1
This criterion was not met as PM2_Supporting has been met.
BP7
This is not a synonymous or non-coding variant.
BP4
The REVEL score = 0.777, which did not meet the ≤ 0.15 threshold required for BP4.
PS2
This variant has not been identified de novo.
PS1
An established pathogenic variant causing this same amino acid change has not been identified.
PS3
No functional evidence has been found for this variant.
PS4
Only 1 proband with POAG had been reported (PMID: 24825108), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting.
PP1
No segregations have been reported for this variant.
PM5
No other missense variants at this amino acid residue have been identified.
PM4
This variant does not cause a protein length change.
PM6
This variant has not been identified de novo.
Approved on: 2022-12-14
Published on: 2022-12-14
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