NM_001065.4(TNFRSF1A):c.295T>C (p.Cys99Arg) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 1, 2017
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:: RCV000214793.23

Allele description [Variation Report for NM_001065.4(TNFRSF1A):c.295T>C (p.Cys99Arg)]

NM_001065.4(TNFRSF1A):c.295T>C (p.Cys99Arg)

Gene:

TNFRSF1A:TNF receptor superfamily member 1A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p13.31

Genomic location:

Preferred name:

NM_001065.4(TNFRSF1A):c.295T>C (p.Cys99Arg)

HGVS:

NC_000012.12:g.6333764A>G
NG_007506.1:g.13332T>C
NM_001065.4:c.295T>CMANE SELECT
NM_001346091.2:c.-30T>C
NM_001346092.2:c.-283T>C
NP_001056.1:p.Cys99Arg
NP_001056.1:p.Cys99Arg
LRG_193t1:c.295T>C
LRG_193:g.13332T>C
LRG_193p1:p.Cys99Arg
NC_000012.11:g.6442930A>G
NM_001065.2:c.295T>C
NM_001065.3:c.295T>C
NR_144351.2:n.557T>C

Protein change:

C99R

Links:

dbSNP: rs104895228

NCBI 1000 Genomes Browser:

rs104895228

Molecular consequence:

NM_001346091.2:c.-30T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001346092.2:c.-283T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001065.4:c.295T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_144351.2:n.557T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000279193	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Mar 4, 2015)	germline	clinical testing	Citation Link,
SCV001247006	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jun 1, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000279193

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Mar 4, 2015)

germline

clinical testing

Citation Link,

SCV001247006

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jun 1, 2017)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000279193.8

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

Description

The C99R missense mutation in the TNFRSF1A gene has been reported previously, as C70R, in association with TRAPS (Aganna et al., 2002). Multiple missense mutations have been reported at this codon (C99Y aka C70Y, C99S aka C70S, and C99G aka C70G) (Simon et al., 2001; Aganna et al., 2003; Horiuchi et al., 2004), which is located in one of the cysteine-rich domain regions of the TNFRSF1A protein and whose substitution likely disrupts normal disulfide bond formation (Masters et al., 2009).

#	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		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001247006.26

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

#	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: Nov 10, 2024

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