The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_000261.2(MYOC):c.1193A>G (p.Lys398Arg)

CA1244064

403218 (ClinVar)

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: 022edf5c-be78-40ba-8860-451d48b81242
Approved on: 2022-05-10
Published on: 2022-05-25

HGVS expressions

NM_000261.2:c.1193A>G
NM_000261.2(MYOC):c.1193A>G (p.Lys398Arg)
NC_000001.11:g.171636247T>C
CM000663.2:g.171636247T>C
NC_000001.10:g.171605387T>C
CM000663.1:g.171605387T>C
NC_000001.9:g.169872010T>C
NG_008859.1:g.21387A>G
ENST00000037502.11:c.1193A>G
ENST00000637303.1:c.235-2383T>C
ENST00000638471.1:c.*531A>G
ENST00000037502.10:c.1193A>G
ENST00000614688.1:c.*157A>G
NM_000261.1:c.1193A>G

Likely Benign

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

Evidence Links 4

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Glaucoma VCEP
The c.1193A>G variant in MYOC is a missense variant predicted to cause substitution of Lysine by Arginine at amino acid 398 (p.Lys398Arg). The highest minor allele frequency of this variant was in the European (non-Finnish) population of gnomAD (v2.1.1) = 0.005978, which met the ≥ 0.001 threshold set for BS1 (772 alleles out of 129,138, meeting the threshold of ≥ 5 of at least 2,000 observed alleles). The REVEL score = 0.207, 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 (PMID: 16466712, 10545602, 11004290) demonstrated that the Lys398Arg 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 BS1 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 met the criteria to receive a score of -6 and to be classified as likely benign (likely benign classification range -2 to -6) for juvenile open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v1, 12 Oct 2021): BS1, BS3_Moderate.
Met criteria codes
BS1
The highest minor allele frequency of this variant was in the European (non-Finnish) population of gnomAD (v2.1.1) = 0.005978, which met the ≥ 0.001 threshold set for BS1 (772 alleles out of 129,138, meeting the threshold of ≥ 5 of at least 2,000 observed alleles).
BS3_Supporting
Applied at the BS3_Moderate level. Previous studies (PMID: 16466712, 10545602, 11004290) demonstrated that the Lys398Arg 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
BP7
This is not a synonymous or non-coding variant.
BP4
The REVEL score = 0.207, 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
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 BS1 was met, PP1 did not apply and segregations were not counted.
PP3
The REVEL score = 0.207, which did not meet the ≥ 0.7 threshold for PP3.
BA1
This criterion was not met as BS1 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.
PM6
This variant has not been identified de novo.
PM2
This criterion was not met as BS1 has been met.
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