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Variant: NM_000261.2(MYOC):c.227G>A (p.Arg76Lys)

CA200294

193066 (ClinVar)

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: cdc28e4e-311a-4cfa-9a12-640c62d568e2

HGVS expressions

NM_000261.2:c.227G>A
NM_000261.2(MYOC):c.227G>A (p.Arg76Lys)
NC_000001.11:g.171652385C>T
CM000663.2:g.171652385C>T
NC_000001.10:g.171621525C>T
CM000663.1:g.171621525C>T
NC_000001.9:g.169888148C>T
NG_008859.1:g.5249G>A
ENST00000037502.11:c.227G>A
ENST00000638471.1:c.130+97G>A
ENST00000037502.10:c.227G>A
ENST00000614688.1:c.227G>A
NM_000261.1:c.227G>A

Benign

Met criteria codes 2
BA1 BS3_Supporting
Not Met criteria codes 13
PS2 PS1 PS3 PS4 PP1 PP3 PM6 PM2 BS1 PM5 PM4 BP4 BP7

Evidence Links 2

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.227G>A variant in MYOC is a missense variant predicted to cause substitution of Arginine by Lysine at amino acid 76 (p.Arg76Lys). The highest minor allele frequency of this variant was in the South Asian population of gnomAD (v2.1.1) = 0.3468, which met the ≥ 0.01 threshold set for BA1 (10,613 alleles out of 30,602, meeting the threshold of ≥ 5 of at least 2,000 observed alleles). The REVEL score = 0.203, which was neither above nor below the thresholds for PP3 (≥ 0.7) or BP4 (≤ 0.15), predicting a damaging or benign impact on MYOC function. Previous studies (PMIDs: 16466712 and 35196929) demonstrated that the Arg76Lys protein had similar solubility and secretion levels to wild type myocilin protein and met the OddsPath threshold for BS3_Moderate (< 0.23), indicating that this variant did not impact protein function. As BA1 was met, PP1 did not apply and segregations were not counted. Although probands with juvenile or primary open angle glaucoma have been reported carrying this variant, PM2_Supporting was not met, therefore PS4 did not apply. In summary, this variant was classified as benign (BA1 is a stand-alone criterion for a benign level of pathogenicity) for juvenile open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v1, 12 Oct 2021): BA1, BS3_Moderate.
Met criteria codes
BA1
The highest minor allele frequency of this variant was in the South Asian population of gnomAD (v2.1.1) = 0.3468, which met the ≥ 0.01 threshold set for BA1 (10,613 alleles out of 30,602, meeting the threshold of ≥ 5 of at least 2,000 observed alleles).
BS3_Supporting
Applied at the BS3_Moderate level. Previous studies (PMIDs: 16466712 and 35196929) demonstrated that the Arg76Lys protein had similar solubility and secretion levels to wild type myocilin protein and met the OddsPath threshold for BS3_Moderate (< 0.23), indicating that this variant did not impact protein function.

Not Met criteria codes
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
This criterion was not met as BS3_Moderate has been met.
PS4
Although probands with JOAG or POAG have been reported carrying this variant, PM2_Supporting was not met, therefore PS4 did not apply.
PP1
As BA1 was met, PP1 did not apply and segregations were not counted.
PP3
The REVEL score = 0.203 which did not meet the ≥ 0.7 threshold required for BP7.
PM6
This variant has not been identified de novo.
PM2
This criterion was not met as BA1 has been met.
BS1
This criterion was not met as BA1 has been met.
PM5
No other missense variants at this amino acid residue have been identified.
PM4
This variant does not cause a protein length change.
BP4
The REVEL score = 0.203, which did not meet the ≤ 0.15 threshold required for BP4.
BP7
This is not a synonymous or non-coding variant.
Approved on: 2022-03-06
Published on: 2022-07-11
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