VCV000190226.2 - ClinVar

NM_017763.6(RNF43):c.394C>T (p.Arg132Ter)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_017763.6(RNF43):c.394C>T (p.Arg132Ter)

Variation ID: 190226 Accession: VCV000190226.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 17q22 17: 58363582 (GRCh38) [ NCBI UCSC ] 17: 56440943 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	May 9, 2015	Jul 22, 2017

HGVS

Nucleotide	Protein	Molecular consequence
NM_017763.6:c.394C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_060233.3:p.Arg132Ter	nonsense
NM_001305544.2:c.394C>T	NP_001292473.1:p.Arg132Ter	nonsense
NM_001305545.1:c.13C>T	NP_001292474.1:p.Arg5Ter	nonsense
NC_000017.11:g.58363582G>A
NC_000017.10:g.56440943G>A
NG_042894.1:g.59001C>T
LRG_1026:g.59001C>T
LRG_1026t1:c.394C>T	LRG_1026p1:p.Arg132Ter

... more HGVS ... less HGVS

Protein change

R132*, R5*

Other names

Canonical SPDI

NC_000017.11:58363581:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA214568 OMIM: 612482.0002 dbSNP: rs786205215 VarSome

Comment on variant

NCBI staff reviewed the sequence information reported in PubMed 27081527 Fig. 1c to determine the location of this allele on the current reference sequence.

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
RNF43		-	-	GRCh38 GRCh37	694	710

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Colon serrated polyposis	Pathogenic (1)	criteria provided, single submitter	-	RCV000170445.1
Sessile serrated polyposis cancer syndrome	Pathogenic (1)	no assertion criteria provided	Jul 19, 2017	RCV000240616.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (-)	criteria provided, single submitter (Submitter's publication) Method: research	Colon Serrated Polyposis Affected status: yes Allele origin: germline	The Canberra Hospital Accession: SCV000222883.1 First in ClinVar: May 09, 2015 Last updated: May 09, 2015	Publications: PubMed (1) PubMed: 22552244 Other databases http://www.nature.com/articles/h… http://www.nature.com/articles/hgv201513 Comment: Mendelian inheritance supported Number of individuals with the variant: 2 Age: 23-27 years Sex: mixed Ethnicity/Population group: Caucasian Geographic origin: Oceania
Pathogenic (Jul 19, 2017)	no assertion criteria provided Method: literature only	SESSILE SERRATED POLYPOSIS CANCER SYNDROME Affected status: not provided Allele origin: germline	OMIM Accession: SCV000299227.2 First in ClinVar: Sep 08, 2016 Last updated: Jul 22, 2017	Publications: PubMed (1) PubMed: 27081527 Comment on evidence: In a brother and sister with sessile serrated polyposis cancer syndrome (SSPCS; 617108), Taupin et al. (2015) identified heterozygosity for a c.2350C-T transition in exon … (more) In a brother and sister with sessile serrated polyposis cancer syndrome (SSPCS; 617108), Taupin et al. (2015) identified heterozygosity for a c.2350C-T transition in exon 2 of the RNF43 gene, resulting in an arg132-to-ter (R132X) substitution at a conserved residue. The mutation was not found in their unaffected father and sister; DNA was unavailable from their mother, who died at age 50 with pancreatic cancer. (less)

Germline Functional Evidence

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 germline classification of this variant

Title	Author	Journal	Year	Link
A deleterious RNF43 germline mutation in a severely affected serrated polyposis kindred.	Taupin D	Human genome variation	2015	PMID: 27081527
Serrated polyposis: the last (or only the latest?) frontier of familial polyposis?	Lanspa SJ	The American journal of gastroenterology	2012	PMID: 22552244
http://www.nature.com/articles/hgv201513	-	-	-	-

Text-mined citations for rs786205215 ...

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 Apr 25, 2022

ClinVar Genomic variation as it relates to human health

NM_017763.6(RNF43):c.394C>T (p.Arg132Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs786205215 ...