NM_198253.3(TERT):c.1499A>T (p.His500Leu) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 31, 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:: RCV002560644.10

Allele description [Variation Report for NM_198253.3(TERT):c.1499A>T (p.His500Leu)]

NM_198253.3(TERT):c.1499A>T (p.His500Leu)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

5p15.33

Genomic location:

Preferred name:

NM_198253.3(TERT):c.1499A>T (p.His500Leu)

HGVS:

NC_000005.10:g.1293387T>A
NG_009265.1:g.6661A>T
NM_001193376.3:c.1499A>T
NM_198253.2:c.1499A>T
NM_198253.3:c.1499A>TMANE SELECT
NP_001180305.1:p.His500Leu
NP_937983.2:p.His500Leu
LRG_343t1:c.1499A>T
LRG_343:g.6661A>T
NC_000005.9:g.1293502T>A
NR_149162.3:n.1578A>T
NR_149163.3:n.1578A>T

Protein change:

H500L

Links:

dbSNP: rs2126683887

NCBI 1000 Genomes Browser:

rs2126683887

Molecular consequence:

NM_001193376.3:c.1499A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198253.3:c.1499A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_149162.3:n.1578A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_149163.3:n.1578A>T - 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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PREDICTED: Homo sapiens calpain 9 (CAPN9), transcript variant X9, mRNA
PREDICTED: Homo sapiens calpain 9 (CAPN9), transcript variant X9, mRNA
gi|2462502374|ref|XM_054333934.1|

Nucleotide
cbBraRuta
cbBraRuta
Brachythecium rutabulum (rough-stalked feathermoss)

BioProject
Aster piccolii voucher FZX0153 external transcribed spacer, partial sequence
Aster piccolii voucher FZX0153 external transcribed spacer, partial sequence
gi|924371507|gb|KP313699.1|

Nucleotide
LOC109950869 [Prunus persica]
LOC109950869 [Prunus persica]
Gene ID:109950869

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002202779	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 31, 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

SCV002202779

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 31, 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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002202779.3

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

Description

This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TERT protein function. ClinVar contains an entry for this variant (Variation ID: 1429673). This variant has not been reported in the literature in individuals affected with TERT-related conditions. This sequence change replaces histidine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 500 of the TERT protein (p.His500Leu).

#	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: Oct 26, 2024

ClinVar

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