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NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg) AND Severe SARS-CoV-2 infection, susceptibility to

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 3, 2021
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001374734.9

Allele description [Variation Report for NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)]

NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)

Gene:
TNFRSF13B:TNF receptor superfamily member 13B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p11.2
Genomic location:
Preferred name:
NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)
HGVS:
  • NC_000017.11:g.16948873A>G
  • NG_007281.1:g.28216T>C
  • NM_012452.3:c.310T>CMANE SELECT
  • NP_036584.1:p.Cys104Arg
  • NP_036584.1:p.Cys104Arg
  • LRG_120t1:c.310T>C
  • LRG_120:g.28216T>C
  • LRG_120p1:p.Cys104Arg
  • NC_000017.10:g.16852187A>G
  • NM_012452.2:c.310T>C
  • NM_012452.3:c.310T>C
  • O14836:p.Cys104Arg
  • p.(Cys104Arg)
Protein change:
C104R; CYS104ARG
Links:
UniProtKB: O14836#VAR_024027; OMIM: 604907.0001; dbSNP: rs34557412
NCBI 1000 Genomes Browser:
rs34557412
Molecular consequence:
  • NM_012452.3:c.310T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Severe SARS-CoV-2 infection, susceptibility to
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001571337Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn
no assertion criteria provided
Likely pathogenic
(Mar 3, 2021) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, SCV001571337.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testingnot provided

Description

This variant was observed in homozygous state in a child with a lethal course of covid-19. The child was also homozygous for a splice site variant in TBK1, that is associated to autoinflammatory disorder. Probably a combination of the deleterious homozygous missense mutation in TNFRSF13B and the homozygous splice site mutation in TBK1 in the presence of an autoinflammatory disease and its treatment regimen - might have promoted the severe disease course observed in the present case either alone or in concert.

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

Last Updated: Nov 3, 2024