NM_007023.4(RAPGEF4):c.922T>C (p.Cys308Arg) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Benign (1 submission)
Last evaluated:: Apr 25, 2018
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:: RCV000892146.3

Allele description

NM_007023.4(RAPGEF4):c.922T>C (p.Cys308Arg)

Gene:

RAPGEF4:Rap guanine nucleotide exchange factor 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.1

Genomic location:

Preferred name:

NM_007023.4(RAPGEF4):c.922T>C (p.Cys308Arg)

HGVS:

NC_000002.12:g.172967362T>C
NM_001100397.2:c.490T>C
NM_001282899.2:c.463T>C
NM_001282900.2:c.409T>C
NM_001282901.2:c.262T>C
NM_001375864.1:c.892T>C
NM_001375865.1:c.922T>C
NM_001375866.1:c.868T>C
NM_001375867.1:c.829T>C
NM_001375868.1:c.922T>C
NM_001375869.1:c.922T>C
NM_001375870.1:c.922T>C
NM_001375871.1:c.868T>C
NM_001375872.1:c.922T>C
NM_001375873.1:c.868T>C
NM_001375874.1:c.868T>C
NM_001375875.1:c.922T>C
NM_001375876.1:c.868T>C
NM_007023.4:c.922T>CMANE SELECT
NP_001093867.1:p.Cys164Arg
NP_001269828.1:p.Cys155Arg
NP_001269829.1:p.Cys137Arg
NP_001269830.1:p.Cys88Arg
NP_001362793.1:p.Cys298Arg
NP_001362794.1:p.Cys308Arg
NP_001362795.1:p.Cys290Arg
NP_001362796.1:p.Cys277Arg
NP_001362797.1:p.Cys308Arg
NP_001362798.1:p.Cys308Arg
NP_001362799.1:p.Cys308Arg
NP_001362800.1:p.Cys290Arg
NP_001362801.1:p.Cys308Arg
NP_001362802.1:p.Cys290Arg
NP_001362803.1:p.Cys290Arg
NP_001362804.1:p.Cys308Arg
NP_001362805.1:p.Cys290Arg
NP_008954.2:p.Cys308Arg
NC_000002.11:g.173832090T>C
NM_007023.3:c.922T>C
NR_164739.1:n.1061T>C
NR_164740.1:n.1007T>C
NR_164741.1:n.1007T>C

Protein change:

C137R

Links:

dbSNP: rs146330323

NCBI 1000 Genomes Browser:

rs146330323

Molecular consequence:

NM_001100397.2:c.490T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282899.2:c.463T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282900.2:c.409T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282901.2:c.262T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375864.1:c.892T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375865.1:c.922T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375866.1:c.868T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375867.1:c.829T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375868.1:c.922T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375869.1:c.922T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375870.1:c.922T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375871.1:c.868T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375872.1:c.922T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375873.1:c.868T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375874.1:c.868T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375875.1:c.922T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375876.1:c.868T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_007023.4:c.922T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_164739.1:n.1061T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164740.1:n.1007T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164741.1:n.1007T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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BioProject Links for Protein (Select 496514435) (1)
BioProject
MULTISPECIES: LysM peptidoglycan-binding domain-containing protein [Peptoniphilu...
MULTISPECIES: LysM peptidoglycan-binding domain-containing protein [Peptoniphilus]
gi|496514435|ref|WP_009222718.1|

Protein
339453[geneid] (275)
ClinVar
platelet-derived growth factor receptor alpha isoform 1 precursor [Mus musculus]
platelet-derived growth factor receptor alpha isoform 1 precursor [Mus musculus]
gi|134032016|ref|NP_001076785.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001036006	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Apr 25, 2018)	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

SCV001036006

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Apr 25, 2018)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001036006.1

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

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

Last Updated: Dec 24, 2023

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