NM_006440.5(TXNRD2):c.11T>C (p.Met4Thr) AND Glucocorticoid deficiency 5

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 21, 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:: RCV004568628.2

Allele description [Variation Report for NM_006440.5(TXNRD2):c.11T>C (p.Met4Thr)]

NM_006440.5(TXNRD2):c.11T>C (p.Met4Thr)

Genes:

COMT:catechol-O-methyltransferase [Gene - OMIM - HGNC]
TXNRD2:thioredoxin reductase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_006440.5(TXNRD2):c.11T>C (p.Met4Thr)

Other names:

p.Met4Thr

HGVS:

NC_000022.11:g.19941793A>G
NG_011526.1:g.5054A>G
NG_011835.1:g.5044T>C
NG_201375.1:g.304A>G
NG_201376.1:g.64A>G
NM_000754.4:c.-196A>GMANE SELECT
NM_001282512.3:c.11T>C
NM_001352300.2:c.11T>C
NM_001362828.2:c.-490A>G
NM_006440.5:c.11T>CMANE SELECT
NP_001269441.1:p.Met4Thr
NP_001339229.1:p.Met4Thr
NP_006431.2:p.Met4Thr
NP_006431.2:p.Met4Thr
LRG_1010t1:c.-196A>G
LRG_417t1:c.11T>C
LRG_1010:g.5054A>G
LRG_417:g.5044T>C
LRG_417p1:p.Met4Thr
NC_000022.10:g.19929316A>G
NM_000754.3:c.-196A>G
NM_006440.3:c.11T>C
NM_006440.4:c.11T>C
NR_147957.2:n.26T>C

Protein change:

M4T

Links:

dbSNP: rs1429174414

NCBI 1000 Genomes Browser:

rs1429174414

Molecular consequence:

NM_000754.4:c.-196A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001362828.2:c.-490A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282512.3:c.11T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001352300.2:c.11T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006440.5:c.11T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_147957.2:n.26T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Glucocorticoid deficiency 5
Identifiers:: MONDO: MONDO:0040502; MedGen: C4540522; OMIM: 617825

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005050211	Clinical Genomics Laboratory, Stanford Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 21, 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

SCV005050211

Clinical Genomics Laboratory, Stanford Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 21, 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	yes	1	not provided	not provided	not provided	not provided	clinical 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 Clinical Genomics Laboratory, Stanford Medicine, SCV005050211.1

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

Description

The p.Met4Thrvariant in the TXNRD2gene has not been previously reported in association with disease. This variantwas absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Computational tools predict that this variant does not impact protein function; however, the accuracy of in silicoalgorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of thep.Met4Thrvariant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PM2; BP4]

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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