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NM_006440.5(TXNRD2):c.1174T>C (p.Tyr392His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 25, 2021)
Last evaluated:
May 6, 2021
Accession:
VCV000263636.12
Variation ID:
263636
Description:
single nucleotide variant
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NM_006440.5(TXNRD2):c.1174T>C (p.Tyr392His)

Allele ID
259121
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
22q11.21
Genomic location
22: 19880630 (GRCh38) GRCh38 UCSC
22: 19868153 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000022.10:g.19868153A>G
NC_000022.11:g.19880630A>G
NG_011835.1:g.66207T>C
... more HGVS
Protein change
Y392H, Y296H, Y391H, Y362H
Other names
-
Canonical SPDI
NC_000022.11:19880629:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00053
Exome Aggregation Consortium (ExAC) 0.00037
The Genome Aggregation Database (gnomAD) 0.00051
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00055
The Genome Aggregation Database (gnomAD), exomes 0.00047
Links
ClinGen: CA10103776
dbSNP: rs201971987
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Feb 26, 2020 RCV000244103.3
Uncertain significance 3 criteria provided, single submitter May 6, 2021 RCV000435580.6
Uncertain significance 1 criteria provided, single submitter May 27, 2020 RCV000467999.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TXNRD2 - - GRCh38
GRCh37
355 753

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Feb 26, 2020)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000318723.5
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Other strong data supporting benign classification;Subpopulation frequency in support of benign classification
Uncertain significance
(May 27, 2020)
criteria provided, single submitter
Method: clinical testing
Primary dilated cardiomyopathy
Allele origin: germline
Invitae
Accession: SCV000546079.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces tyrosine with histidine at codon 392 of the TXNRD2 protein (p.Tyr392His). The tyrosine residue is highly conserved and there is a … (more)
Uncertain significance
(May 06, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000532171.4
Submitted: (Sep 25, 2021)
Evidence details
Comment:
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious … (more)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001743025.3
Submitted: (Sep 02, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001975275.1
Submitted: (Sep 21, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811
Post-mortem whole-exome analysis in a large sudden infant death syndrome cohort with a focus on cardiovascular and metabolic genetic diseases. Neubauer J European journal of human genetics : EJHG 2017 PMID: 28074886

Text-mined citations for rs201971987...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021