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


Variant: NM_000261.2(MYOC):c.1102C>T (p.Gln368Ter)

CA119172

7949 (ClinVar)

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: 399db6af-6807-459a-9953-39c259125cad
Approved on: 2022-03-07
Published on: 2022-07-11

HGVS expressions

NM_000261.2:c.1102C>T
NM_000261.2(MYOC):c.1102C>T (p.Gln368Ter)
NC_000001.11:g.171636338G>A
CM000663.2:g.171636338G>A
NC_000001.10:g.171605478G>A
CM000663.1:g.171605478G>A
NC_000001.9:g.169872101G>A
NG_008859.1:g.21296C>T
ENST00000037502.11:c.1102C>T
ENST00000637303.1:c.235-2292G>A
ENST00000638471.1:c.*440C>T
ENST00000037502.10:c.1102C>T
ENST00000614688.1:c.*66C>T
NM_000261.1:c.1102C>T
More

Pathogenic

Met criteria codes 4
PS4 PS3_Moderate PM4 PP1_Strong
Not Met criteria codes 11
PS2 PS1 PM5 BA1 PM6 PM2 PP3 BS3 BS1 BP7 BP4

Evidence Links 1

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.1102C>T variant in MYOC is predicted to cause a change in the length of the protein due to the insertion of a terminating codon instead of the usual Glutamine at amino acid 368 (p.Gln368Ter). This variant is predicted to cause a deletion of ≥ 10% of the protein within the conserved olfactomedin domain, meeting PM4. Although this variant had a minor allele frequency of 0.003344 in the European (Finnish) population of gnomAD (84 alleles out of 25,118), which meets the ≥ 0.001 threshold for BS1, Gln368Ter is exempt from this criterion due to its incomplete penetrance and the presence of a common disease haplotype in all carriers. There was no computational evidence predicting a damaging or benign impact of this variant on MYOC function. This variant is exempt from the rule which normally does not allow the application of PS4 unless PM2_Supporting is met. 23 probands with juvenile or primary open angle glaucoma (JOAG or POAG) have been reported carrying this variant (PMIDs: 11535458, 11004290, 10815160, 22736945, 11803488, 12189160), which met PS4 (≥ 15 probands). As this variant is exempt from the application of BS1, PP1 has been applied. 52 segregations in 10 families, with JOAG or POAG, have been reported (PMIDs: 11004290, 10815160, 11535458), which fulfilled PP1_Strong (≥ 7 meioses in > 1 family). There were many more probands and family studies published than presented here. A previous study (PMID: 16466712) demonstrated that the Gln368Ter protein had reduced secretion levels compared to wild type myocilin protein and met the OddsPath threshold for PS3_Moderate (> 4.3), indicating that this variant did impact protein function. In summary, this variant met the criteria to receive a score of 12 and to be classified as pathogenic (pathogenic classification ≥ 10) for juvenile open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v1, 12 Oct 2021): PS4, PP1_Strong, PM4, PS3_Moderate.
Met criteria codes
PS4
This variant is exempt from the rule which normally does not allow the application of PS4 unless PM2_Supporting is met. 23 probands with JOAG or POAG have been reported carrying this variant (PMIDs: 11535458, 11004290, 10815160, 22736945, 11803488, 12189160), which met PS4 (≥15 probands). There were many more probands published than presented here.
PS3_Moderate
A previous study (PMID: 16466712) demonstrated that the Gln368Ter protein had reduced secretion levels compared to wild type myocilin protein and met the OddsPath threshold for PS3_Moderate (> 4.3), indicating that this variant did impact protein function.

PM4
This truncating variant is predicted to cause a deletion of ≥ 10% of the protein and is within the conserved olfactomedin domain.
PP1_Strong
As this variant is exempt from the application of BS1, PP1 has been applied. 52 segregations in 10 families, with JOAG or POAG, have been reported (PMIDs: 11004290, 10815160, 11535458), which fulfilled PP1_Strong (≥ 7 meioses in > 1 family). There were many more family studies published than presented here.
Not Met criteria codes
PS2
This variant has not been identified de novo.
PS1
This variant does not involve an amino acid change.
PM5
This is not a missense variant.
BA1
This variant did not meet the ≥ 0.01 minor allele frequency threshold in gnomAD (v2.1.1).
PM6
This variant has not been identified de novo.
PM2
The highest minor allele frequency of this variant was in the European (Finnish) population of gnomAD (v2.1.1) = 0.003344 (84 alleles out of 25,118), which did not meet the ≤ 0.0001 threshold set for PM2_Supporting.
PP3
This is not a missense variant.
BS3
This criterion was not met as PS3_Moderate has been met.
BS1
Although this variant had a minor allele frequency of 0.003344 in the European (Finnish) population of gnomAD (84 alleles out of 25,118), which meets the ≥ 0.001 threshold for BS1, Gln368Ter is exempt from this criterion due to its incomplete penetrance and the presence of a common disease haplotype in all carriers.
BP7
This is not a synonymous or non-coding variant.
BP4
This is not a missense, synonymous or non-coding variant.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.