NM_198253.3(TERT):c.3302C>T (p.Thr1101Met) AND Dyskeratosis congenita

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 28, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002256386.10

Allele description [Variation Report for NM_198253.3(TERT):c.3302C>T (p.Thr1101Met)]

NM_198253.3(TERT):c.3302C>T (p.Thr1101Met)

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.3302C>T (p.Thr1101Met)

HGVS:

NC_000005.10:g.1253825G>A
NG_009265.1:g.46223C>T
NM_001193376.3:c.3113C>T
NM_198253.3:c.3302C>TMANE SELECT
NP_001180305.1:p.Thr1038Met
NP_937983.2:p.Thr1101Met
NP_937983.2:p.Thr1101Met
LRG_343t1:c.3302C>T
LRG_343:g.46223C>T
LRG_343p1:p.Thr1101Met
NC_000005.9:g.1253940G>A
NM_198253.2:c.3302C>T
NR_149162.3:n.3010C>T
NR_149163.3:n.2974C>T

Protein change:

T1038M

Links:

dbSNP: rs764602705

NCBI 1000 Genomes Browser:

rs764602705

Molecular consequence:

NM_001193376.3:c.3113C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198253.3:c.3302C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_149162.3:n.3010C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_149163.3:n.2974C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Dyskeratosis congenita
Identifiers:: MONDO: MONDO:0015780; MedGen: C0265965; OMIM: PS127550

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002533152	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Uncertain significance (May 28, 2021)	germline	curation	Citation Link,
SCV002611248	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Feb 28, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002533152

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Uncertain significance
(May 28, 2021)

germline

curation

Citation Link,

SCV002611248

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Feb 28, 2022)

germline

clinical testing

Citation Link

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, curation

Details of each submission

From Sema4, Sema4, SCV002533152.1

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

#	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

From Ambry Genetics, SCV002611248.2

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

Description

The p.T1101M variant (also known as c.3302C>T), located in coding exon 16 of the TERT gene, results from a C to T substitution at nucleotide position 3302. The threonine at codon 1101 is replaced by methionine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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 24, 2024

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