NM_198253.3(TERT):c.1313C>A (p.Pro438His) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 17, 2021
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:: RCV002552970.10

Allele description [Variation Report for NM_198253.3(TERT):c.1313C>A (p.Pro438His)]

NM_198253.3(TERT):c.1313C>A (p.Pro438His)

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.1313C>A (p.Pro438His)

HGVS:

NC_000005.10:g.1293573G>T
NG_009265.1:g.6475C>A
NM_001193376.3:c.1313C>A
NM_198253.3:c.1313C>AMANE SELECT
NP_001180305.1:p.Pro438His
NP_937983.2:p.Pro438His
LRG_343:g.6475C>A
NC_000005.9:g.1293688G>T
NR_149162.3:n.1392C>A
NR_149163.3:n.1392C>A

Protein change:

P438H

Links:

dbSNP: rs2126684855

NCBI 1000 Genomes Browser:

rs2126684855

Molecular consequence:

NM_001193376.3:c.1313C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_198253.3:c.1313C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_149162.3:n.1392C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_149163.3:n.1392C>A - 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

Clear Turn Off Turn On

RNU6-1315P RNA, U6 small nuclear 1315, pseudogene [Homo sapiens]
RNU6-1315P RNA, U6 small nuclear 1315, pseudogene [Homo sapiens]
Gene ID:106481950

Gene

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
SCV002151304	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 17, 2021)	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

SCV002151304

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 17, 2021)

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, SCV002151304.3

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

Description

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 sequence change replaces proline with histidine at codon 438 of the TERT protein (p.Pro438His). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and histidine. This variant has not been reported in the literature in individuals affected with TERT-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0").

#	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

ClinVar

Relating variation to medicine