The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • ClinVar Id was derived from the Allele Registry.
  • There was no gene found in the curated document received from the VCI/VCEP
  • Gene listed was thus derived from ClinVar and/or CAR


Variant: NM_000261.2:c.1008del

CA1139655085

1342199 (ClinVar)

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: 46c972a6-9c83-4492-ab2e-1afda05165a1

HGVS expressions

NM_000261.2:c.1008del
NC_000001.11:g.171636432del
CM000663.2:g.171636432del
NC_000001.10:g.171605572del
CM000663.1:g.171605572del
NC_000001.9:g.169872195del
NG_008859.1:g.21203del
ENST00000037502.11:c.1009del
ENST00000637303.1:c.235-2198del
ENST00000638471.1:c.*347del
ENST00000037502.10:c.1009del
ENST00000614688.1:c.1009-1del
NM_000261.1:c.1009del
NM_000261.2:c.1009del
NM_000261.2(MYOC):c.1009del (p.Gln337fs)

Uncertain Significance

Met criteria codes 3
PM2_Supporting PP1_Moderate PM4
Not Met criteria codes 12
PS2 PS1 PS3 PS4 PP3 BA1 PM6 BS3 BS1 PM5 BP4 BP7

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Glaucoma VCEP
The c.1009delC variant in MYOC is a deletion of a single nucleotide, predicted to encode a frameshift with consequent premature termination of the protein at codon 9 of the frameshift, or amino acid 346 (p.Gln337ArgfsTer9). This variant is predicted to cause a deletion of ≥ 10% of the protein within the conserved olfactomedin domain (PM4). 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. There was no computational or functional evidence predicting a damaging or benign impact of this variant on MYOC function. 14 segregations in 1 family, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMID: 18776955), which fulfilled PP1_Moderate (≥5 meioses in ≥1 family, but not the ≥7 meioses in >1 family for the strong criterion). Only 1 proband with JOAG had been reported (PMID: 18776955), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting. In summary, this variant met the criteria to receive a score of 5 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): PM4, PP1_Moderate, PM2_Supporting
Met criteria codes
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.
PP1_Moderate
14 segregations in 1 family, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMID: 18776955), which fulfilled PP1_Moderate (≥5 meioses in ≥1 family, but not the ≥7 meioses in >1 family for the strong criterion).
PM4
This truncating variant is predicted to cause a deletion of ≥ 10% of the protein and is within the conserved olfactomedin domain.
Not Met criteria codes
PS2
This variant has not been identified de novo.
PS1
This variant does not involve an amino acid change.
PS3
No functional evidence has been found for this variant.
PS4
Only 1 proband with JOAG had been reported (PMID: 18776955), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting.
PP3
This is not a missense variant.
BA1
This criterion was not met as PM2_Supporting has been met.
PM6
This variant has not been identified de novo.
BS3
No functional evidence has been found for this variant.
BS1
This criterion was not met as PM2_Supporting has been met.
PM5
This is not a missense variant.
BP4
This is not a missense, synonymous or non-coding variant.
BP7
This is not a synonymous or non-coding variant.
Approved on: 2022-02-21
Published on: 2022-07-11
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