NM_198253.3(TERT):c.1174_1175del (p.Leu392fs) AND TERT-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 24, 2023
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:: RCV004527915.1

Allele description [Variation Report for NM_198253.3(TERT):c.1174_1175del (p.Leu392fs)]

NM_198253.3(TERT):c.1174_1175del (p.Leu392fs)

Gene:

TERT:telomerase reverse transcriptase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5p15.33

Genomic location:

Preferred name:

NM_198253.3(TERT):c.1174_1175del (p.Leu392fs)

HGVS:

NC_000005.10:g.1293711_1293712del
NG_009265.1:g.6336_6337del
NM_001193376.3:c.1174_1175del
NM_003219.1:c.1174_1175delCT
NM_198253.3:c.1174_1175delMANE SELECT
NP_001180305.1:p.Leu392fs
NP_003210.1:p.Leu392Valfs
NP_937983.2:p.Leu392Valfs
NP_937983.2:p.Leu392fs
LRG_343t1:c.1174_1175del
LRG_343:g.6336_6337del
LRG_343p1:p.Leu392Valfs
NC_000005.9:g.1293826_1293827del
NM_198253.2:c.1174_1175delCT
NR_149162.3:n.1253_1254del
NR_149163.3:n.1253_1254del

Protein change:

L392fs

Molecular consequence:

NM_001193376.3:c.1174_1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003219.1:c.1174_1175delCT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_198253.3:c.1174_1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_149162.3:n.1253_1254del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_149163.3:n.1253_1254del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: TERT-related disorder
Synonyms:: TERT-Related Disorders; TERT-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004102894	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 24, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004102894

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 24, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	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 PreventionGenetics, part of Exact Sciences, SCV004102894.1

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

Description

The TERT c.1174_1175delCT variant is predicted to result in a frameshift and premature protein termination (p.Leu392Valfs*146). The p.Leu392Valfs*146 variant was reported in an individual with prostate cancer and lymphoma. This individual also had a shortened telomere length (less than 1st percentile tested in granulocytes, Walsh et al. 2019. PubMed ID: 32923861). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Frameshift variants in TERT are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Nov 3, 2024

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