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Variant: NM_000261.2(MYOC):c.1440C>A (p.Asn480Lys)

CA119175

7951 (ClinVar)

Gene: MYOC
Condition: juvenile open angle glaucoma
Inheritance Mode: Autosomal dominant inheritance
UUID: d0adf58d-a397-461c-b1cd-9d3a527bd978
Approved on: 2022-05-10
Published on: 2022-05-25

HGVS expressions

NM_000261.2:c.1440C>A
NM_000261.2(MYOC):c.1440C>A (p.Asn480Lys)
NC_000001.11:g.171636000G>T
CM000663.2:g.171636000G>T
NC_000001.10:g.171605140G>T
CM000663.1:g.171605140G>T
NC_000001.9:g.169871763G>T
NG_008859.1:g.21634C>A
ENST00000037502.11:c.1440C>A
ENST00000637303.1:c.235-2630G>T
ENST00000638471.1:c.*778C>A
ENST00000037502.10:c.1440C>A
ENST00000614688.1:c.*404C>A
NM_000261.1:c.1440C>A

Pathogenic

Met criteria codes 5
PP1_Strong PM2_Supporting PP3 PS3_Moderate PS4_Moderate
Not Met criteria codes 10
BA1 PM6 PM5 PM4 BS3 BS1 PS2 PS1 BP7 BP4

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Glaucoma VCEP
The c.1440C>A 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. Over 90 segregations in 8 families, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMIDs: 12107514, 24883016, 9556305), which fulfilled PP1_Strong (≥ 7 meioses in > 1 family). 13 probands with JOAG or POAG have been reported carrying this variant (PMIDs: pers. communication E Souzeau, 22194650, 12872267, 12107514, 24883016, 9556305), which met PS4_Moderate (≥ 6 probands). In summary, this variant met the criteria to receive a score of 10 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): PP1_Strong, PS3_Moderate, PS4_Moderate, PP3, PM2_Supporting.
Met criteria codes
PP1_Strong
Over 90 segregations in 8 families, with juvenile or primary open angle glaucoma (JOAG or POAG), have been reported (PMIDs: 12107514, 24883016, 9556305), which fulfilled PP1_Strong (≥ 7 meioses in > 1 family).
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.
PP3
The REVEL score = 0.784, which met the ≥ 0.7 threshold for PP3, predicting a damaging effect on MYOC function.
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.

PS4_Moderate
13 probands with JOAG or POAG have been reported carrying this variant (PMIDs: pers. communication E Souzeau, 22194650, 12872267, 12107514, 24883016, 9556305), which met PS4_Moderate (≥ 6 probands).
Not Met criteria codes
BA1
This criterion was not met as PM2_Supporting has been met.
PM6
This variant has not been identified de novo.
PM5
No other missense variants at this amino acid residue have been identified.
PM4
This variant does not cause a protein length change.
BS3
This criterion was not met as PS3_Moderate has been met.
BS1
This criterion was not met as PM2_Supporting has been met.
PS2
This variant has not been identified de novo.
PS1
The same amino acid change (p.Asn480Lys), resulting from a different nucleotide change (c.1440C>G) (PMID: 18303389), was not classified as pathogenic or likely pathogenic by the ClinGen Glaucoma VCEP without the use of PS1. This variant (c.1440C>A, p.Asn480Lys, ClinVarID: 7951) is used to apply PS1 to the other nucleotide change variant located at this amino acid position (c.1440C>G, p.Asn480Lys, PMID: 18303389).
BP7
This is not a synonymous or non-coding variant.
BP4
This criterion was not met as PP3 has been met.
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