NM_000459.5(TEK):c.470_471insTGGT (p.Lys157fs) AND Glaucoma 3, primary congenital, E

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 3, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001808096.2

Allele description [Variation Report for NM_000459.5(TEK):c.470_471insTGGT (p.Lys157fs)]

NM_000459.5(TEK):c.470_471insTGGT (p.Lys157fs)

Gene:

TEK:TEK receptor tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

9p21.2

Genomic location:

Preferred name:

NM_000459.5(TEK):c.470_471insTGGT (p.Lys157fs)

HGVS:

NC_000009.12:g.27168600_27168601insTGGT
NG_011828.1:g.64452_64453insTGGT
NG_011828.2:g.64461_64462insTGGT
NM_000459.5:c.470_471insTGGTMANE SELECT
NM_001290077.2:c.470_471insTGGT
NM_001290078.2:c.158_159insTGGT
NM_001375475.1:c.470_471insTGGT
NM_001375476.1:c.470_471insTGGT
NP_000450.3:p.Lys157fs
NP_001277006.1:p.Lys157fs
NP_001277006.2:p.Lys157Asnfs
NP_001277007.1:p.Lys53fs
NP_001277007.2:p.Lys53Asnfs
NP_001362404.1:p.Lys157fs
NP_001362405.1:p.Lys157fs
NC_000009.11:g.27168598_27168599insTGGT
NM_001290077.1:c.470_471insTGGT
NM_001290078.1:c.158_159insTGGT

Protein change:

K157fs

Links:

dbSNP: rs2131141182

NCBI 1000 Genomes Browser:

rs2131141182

Molecular consequence:

NM_000459.5:c.470_471insTGGT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001290077.2:c.470_471insTGGT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001290078.2:c.158_159insTGGT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375475.1:c.470_471insTGGT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375476.1:c.470_471insTGGT - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Glaucoma 3, primary congenital, E (GLC3E)
Identifiers:: MONDO: MONDO:0014998; MedGen: C4310639; OMIM: 617272

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002058565	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 3, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003936894	Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana	no assertion criteria provided	Pathogenic	germline	research

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002058565

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 3, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003936894

Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana

no assertion criteria provided

Pathogenic

germline

research

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	1	not provided	research, clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV002058565.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana, SCV003936894.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	research	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 1, 2024

ClinVar

Relating variation to medicine