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NM_000261.2(MYOC):c.855G>T (p.Thr285=) AND Glaucoma of childhood

Germline classification:
Benign (1 submission)
Last evaluated:
Feb 7, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001824131.11

Allele description [Variation Report for NM_000261.2(MYOC):c.855G>T (p.Thr285=)]

NM_000261.2(MYOC):c.855G>T (p.Thr285=)

Gene:
MYOC:myocilin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q24.3
Genomic location:
Preferred name:
NM_000261.2(MYOC):c.855G>T (p.Thr285=)
Other names:
NM_000261.2(MYOC):c.855G>T; p.Thr285=
HGVS:
  • NC_000001.11:g.171636585C>A
  • NG_008859.1:g.21049G>T
  • NM_000261.2:c.855G>TMANE SELECT
  • NP_000252.1:p.Thr285=
  • NC_000001.10:g.171605725C>A
  • NC_000001.10:g.171605725C>A
  • NM_000261.1:c.855G>T
Links:
dbSNP: rs146606638
NCBI 1000 Genomes Browser:
rs146606638
Molecular consequence:
  • NM_000261.2:c.855G>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Glaucoma of childhood
Synonyms:
Childhood glaucoma; Infantile glaucoma; Pediatric glaucoma; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0020367; MedGen: C2981140; Human Phenotype Ontology: HP:0001087

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002073865ClinGen Glaucoma Variant Curation Expert Panel
reviewed by expert panel

(ClinGen Glaucoma ACMG Specifications v1.1)		Benign
(Feb 7, 2022) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Glaucoma Variant Curation Expert Panel, SCV002073865.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.855G>T variant in MYOC is a synonymous variant (p.Thr285=). The highest minor allele frequency of this variant was in the European (Finnish) population of gnomAD (v2.1.1) = 0.01891, which met the >= 0.01 threshold set for BA1 (471 alleles out of 24 902, meeting the threshold of >= 5 of at least 2,000 observed alleles). This variant was not predicted to affect splicing, as assessed with SpliceAI (<= 0.2), with a CADD score (v1.6) = 0.286 which met the <= 10 threshold for BP4, and the GERP score = -7.62 (threshold < 0), indicating a lack of conservation at this site (BP7). This evidence suggests that the variant does not impact MYOC function. As BA1 was met, PP1 did not apply and segregations were not counted. Although probands with juvenile or primary open angle glaucoma have been reported carrying this variant, PM2_Supporting was not met, therefore PS4 did not apply. In summary, this variant was classified as benign (BA1 is a stand-alone criterion for a benign level of pathogenicity) for juvenile open angle glaucoma based on the ACMG/AMP criteria met, as specified by the ClinGen Glaucoma VCEP (v1, 12 Oct 2021): BA1, BP4, BP7.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024