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Variant: NM_000261.2(MYOC):c.1196G>T (p.Gly399Val)

CA119182

7957 (ClinVar)

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: 7543f7e0-692c-4ce1-867a-c57c1f97d9a2

HGVS expressions

NM_000261.2:c.1196G>T
NM_000261.2(MYOC):c.1196G>T (p.Gly399Val)
NC_000001.11:g.171636244C>A
CM000663.2:g.171636244C>A
NC_000001.10:g.171605384C>A
CM000663.1:g.171605384C>A
NC_000001.9:g.169872007C>A
NG_008859.1:g.21390G>T
ENST00000037502.11:c.1196G>T
ENST00000637303.1:c.235-2386C>A
ENST00000638471.1:c.*534G>T
ENST00000037502.10:c.1196G>T
ENST00000614688.1:c.*160G>T
NM_000261.1:c.1196G>T

Uncertain Significance

Met criteria codes 2
PP1_Moderate PP3
Not Met criteria codes 13
PM4 PM5 PM6 PM2 BS3 BS1 BP4 BP7 PS2 PS3 PS1 PS4 BA1

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Glaucoma VCEP
The c.1196G>T variant in MYOC is a missense variant predicted to cause substitution of Glycine by Valine at amino acid 399 (p.Gly399Val). The highest minor allele frequency of this variant was in the Latino/Admixed American population of gnomAD (v2.1.1) = 0.0001156 (4 alleles out of 34,592), which did not meet the PM2_Supporting allele frequency threshold (≤ 0.0001) or the BS1 allele frequency threshold (≥ 0.001). The REVEL score = 0.968, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function. There was no functional evidence predicting a damaging or benign impact of this variant on MYOC function. 10 segregations in 1 family, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMID: 11774072), which fulfilled PP1_Moderate (5-6 meioses). Although a proband with JOAG had 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 3 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): PP1_Moderate, PP3.
Met criteria codes
PP1_Moderate
10 segregations in 1 family, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMID: 11774072), which fulfilled PP1_Moderate (5-6 meioses).
PP3
The REVEL score = 0.968, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function.
Not Met criteria codes
PM4
This variant does not cause a protein length change.
PM5
PM5_Supporting could not be applied to this variant as the other missense variant at the same amino acid residue (c.1196G>A, p.Gly399Asp, PMID: 17562996) was not classified as likely pathogenic or pathogenic.
PM6
This variant has not been identified de novo.
PM2
The highest minor allele frequency of this variant was in the Latino/Admixed American population of gnomAD (v2.1.1) = 0.0001156 (4 alleles out of 34,592), which did not meet the ≤ 0.0001 threshold set for PM2_Supporting.
BS3
No functional evidence has been found for this variant.
BS1
The highest minor allele frequency of this variant was in the Latino/Admixed American population of gnomAD (v2.1.1) = 0.0001156 (4 alleles out of 34,592), which did not meet the ≥ 0.001 threshold nor the ≥5 alleles necessary to meet BS1.
BP4
This criterion was not met as PP3 has been met.
BP7
This is not a synonymous or non-coding variant.
PS2
This variant has not been identified de novo.
PS3
No functional evidence has been found for this variant.
PS1
An established pathogenic variant causing this same amino acid change has not been identified.
PS4
Although a proband with JOAG had been reported carrying this variant, PM2_Supporting was not met, therefore PS4 did not apply.
BA1
This variant did not meet the ≥ 0.01 minor allele frequency threshold in gnomAD (v2.1.1).
Approved on: 2022-12-14
Published on: 2022-12-14
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