NM_198253.3(TERT):c.1314del (p.Glu439fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 9, 2020
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:: RCV002550260.10

Allele description [Variation Report for NM_198253.3(TERT):c.1314del (p.Glu439fs)]

NM_198253.3(TERT):c.1314del (p.Glu439fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

5p15.33

Genomic location:

Preferred name:

NM_198253.3(TERT):c.1314del (p.Glu439fs)

HGVS:

NC_000005.10:g.1293576del
NG_009265.1:g.6476del
NM_001193376.3:c.1314del
NM_198253.3:c.1314delMANE SELECT
NP_001180305.1:p.Glu439fs
NP_937983.2:p.Glu439fs
LRG_343:g.6476del
NC_000005.9:g.1293687del
NC_000005.9:g.1293691del
NR_149162.3:n.1393del
NR_149163.3:n.1393del

Protein change:

E439fs

Links:

dbSNP: rs2126684848

NCBI 1000 Genomes Browser:

rs2126684848

Molecular consequence:

NM_001193376.3:c.1314del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_198253.3:c.1314del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_149162.3:n.1393del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_149163.3:n.1393del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Dyskeratosis congenita, autosomal dominant 2
Identifiers:: MONDO: MONDO:0013521; MedGen: C3151443; OMIM: 613989

Name:: Idiopathic Pulmonary Fibrosis
Synonyms:: Idiopathic fibrosing alveolitis, chronic form
Identifiers:: MeSH: D054990; MedGen: C1800706

Recent activity

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RecName: Full=Desiccation-related protein clone PCC6-19; AltName: Full=CDET6-19
RecName: Full=Desiccation-related protein clone PCC6-19; AltName: Full=CDET6-19
gi|118518|sp|P22239.1|DHB_CRAPL

Protein
RecName: Full=Desiccation-related protein clone PCC27-04
RecName: Full=Desiccation-related protein clone PCC27-04
gi|118517|sp|P22238.1|DHA_CRAPL

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001579352	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 9, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16247010, 17460043, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001579352

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 9, 2020)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Haploinsufficiency of telomerase reverse transcriptase leads to anticipation in autosomal dominant dyskeratosis congenita.

Armanios M, Chen JL, Chang YP, Brodsky RA, Hawkins A, Griffin CA, Eshleman JR, Cohen AR, Chakravarti A, Hamosh A, Greider CW.

Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15960-4. Epub 2005 Oct 24.

PubMed [citation]

PMID:: 16247010
PMCID:: PMC1276104

Adult-onset pulmonary fibrosis caused by mutations in telomerase.

Tsakiri KD, Cronkhite JT, Kuan PJ, Xing C, Raghu G, Weissler JC, Rosenblatt RL, Shay JW, Garcia CK.

Proc Natl Acad Sci U S A. 2007 May 1;104(18):7552-7. Epub 2007 Apr 25.

PubMed [citation]

PMID:: 17460043
PMCID:: PMC1855917

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001579352.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Glu439Argfs*70) in the TERT gene. It is expected to result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has not been reported in the literature in individuals with TERT-related conditions. Loss-of-function variants in TERT are known to be pathogenic (PMID: 16247010, 17460043). For these reasons, this variant has been classified 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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