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NM_001283009.2(RTEL1):c.1301C>T (p.Thr434Met) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Nov 1, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV001508902.13

Allele description [Variation Report for NM_001283009.2(RTEL1):c.1301C>T (p.Thr434Met)]

NM_001283009.2(RTEL1):c.1301C>T (p.Thr434Met)

Genes:
RTEL1-TNFRSF6B:RTEL1-TNFRSF6B readthrough (NMD candidate) [Gene - HGNC]
RTEL1:regulator of telomere elongation helicase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.33
Genomic location:
Preferred name:
NM_001283009.2(RTEL1):c.1301C>T (p.Thr434Met)
HGVS:
  • NC_000020.11:g.63685825C>T
  • NG_033901.1:g.33016C>T
  • NM_001283009.2:c.1301C>TMANE SELECT
  • NM_001283010.1:c.632C>T
  • NM_016434.4:c.1301C>T
  • NM_032957.5:c.1373C>T
  • NP_001269938.1:p.Thr434Met
  • NP_001269938.1:p.Thr434Met
  • NP_001269939.1:p.Thr211Met
  • NP_057518.1:p.Thr434Met
  • NP_116575.3:p.Thr458Met
  • NP_116575.3:p.Thr458Met
  • LRG_1149t1:c.1373C>T
  • LRG_1149t2:c.1301C>T
  • LRG_1149t3:c.1301C>T
  • LRG_1149:g.33016C>T
  • LRG_1149p1:p.Thr458Met
  • LRG_1149p2:p.Thr434Met
  • LRG_1149p3:p.Thr434Met
  • NC_000020.10:g.62317178C>T
  • NM_001283009.1:c.1301C>T
  • NM_032957.4:c.1373C>T
  • NR_037882.1:n.2128C>T
  • p.Thr458Met
Protein change:
T211M
Links:
dbSNP: rs77086616
NCBI 1000 Genomes Browser:
rs77086616
Molecular consequence:
  • NM_001283009.2:c.1301C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001283010.1:c.632C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_016434.4:c.1301C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032957.5:c.1373C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_037882.1:n.2128C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
7

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001715338Mayo Clinic Laboratories, Mayo Clinic
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Oct 5, 2022)
germlineclinical testing

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

SCV002576928GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Mar 28, 2022)
germlineclinical testing

Citation Link,

SCV004183930CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(Nov 1, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknown6not providednot providednot providednot providedclinical 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 Mayo Clinic Laboratories, Mayo Clinic, SCV001715338.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided6not providednot providedclinical testing PubMed (1)

Description

BS1

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided6not providednot providednot provided

From GeneDx, SCV002576928.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Identified with another RTEL1 variant in a patient with severe aplastic anemia (Ghemlas 2015); This variant is associated with the following publications: (PMID: 26136524, 30462709)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV004183930.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

RTEL1: BP4

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 9, 2024