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

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Variant: NM_000261.2:c.1440C>G

CA343723150

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: 34165818-5669-4223-ae50-86064c1ea325
Approved on: 2022-05-10
Published on: 2022-05-25

HGVS expressions

NM_000261.2:c.1440C>G
NC_000001.11:g.171636000G>C
CM000663.2:g.171636000G>C
NC_000001.10:g.171605140G>C
CM000663.1:g.171605140G>C
NC_000001.9:g.169871763G>C
NG_008859.1:g.21634C>G
ENST00000037502.11:c.1440C>G
ENST00000637303.1:c.235-2630G>C
ENST00000638471.1:c.*778C>G
ENST00000037502.10:c.1440C>G
ENST00000614688.1:c.*404C>G
NM_000261.1:c.1440C>G

Likely Pathogenic

Met criteria codes 5
PS3_Moderate PS1 PP1 PP3 PM2_Supporting
Not Met criteria codes 10
BS3 BS1 BP7 BP4 PS2 PS4 BA1 PM4 PM5 PM6

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Glaucoma VCEP
The c.1440C>G variant in MYOC is a missense variant predicted to cause substitution of Asparagine by Lysine at amino acid 480 (p.Asn480Lys). 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. The REVEL score = 0.784, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function. Previous studies (PMIDs: 16466712 and 35196929) demonstrated that the Asn480Lys protein had increased insolubility and 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. 4 segregations in 1 family, with juvenile open angle glaucoma (JOAG), have been reported (PMID: 18303389), which fulfilled PP1 (3-4 meioses). Only 1 proband with JOAG had been reported (PMID: 18303389), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting. The same amino acid change (p.Asn480Lys), resulting from a different nucleotide change (c.1440C>A, ClinVarID: 7951), was classified as pathogenic for JOAG by the ClinGen Glaucoma VCEP. This variant was not predicted to affect splicing, as assessed with SpliceAI (≤ 0.2) (PS1). In summary, this variant met the criteria to receive a score of 9 and to be classified as likely pathogenic (likely pathogenic classification range 6 to 9) for juvenile open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v1, 12 Oct 2021): PS1, PS3_Moderate, PP1, PP3, PM2_Supporting.
Met criteria codes
PS3_Moderate
Previous studies (PMIDs: 16466712 and 35196929) demonstrated that the Asn480Lys protein had increased insolubility and 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.

PS1
The same amino acid change (p.Asn480Lys), resulting from a different nucleotide change (c.1440C>A, ClinVarID: 7951), was classified as pathogenic for juvenile open angle glaucoma by the ClinGen Glaucoma VCEP. This variant is not predicted to affect splicing, as assessed with SpliceAI (≤ 0.2).
PP1
4 segregations in 1 family, with JOAG, have been reported (PMID: 18303389), which fulfilled PP1 (3-4 meioses).
PP3
The REVEL score = 0.784, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function.
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.
Not Met criteria codes
BS3
This criterion was not met as PS3_Moderate has been met.
BS1
This criterion was not met as PM2_Supporting has been met.
BP7
This is not a synonymous or non-coding variant.
BP4
This criterion was not met as PP3 has been met.
PS2
This variant has not been identified de novo.
PS4
Only 1 proband with JOAG had been reported (PMID: 18303389), not meeting the ≥ 2 probands threshold required to meet PS4_Supporting.
BA1
This criterion was not met as PM2_Supporting has been met.
PM4
This variant does not cause a protein length change.
PM5
No other missense variants at this amino acid residue have been identified.
PM6
This variant has not been identified de novo.
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