NM_007023.4(RAPGEF4):c.1546A>G (p.Ile516Val) AND not provided

Germline classification:: Benign (2 submissions)
Last evaluated:: Jun 6, 2018
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:: RCV000972383.4

Allele description [Variation Report for NM_007023.4(RAPGEF4):c.1546A>G (p.Ile516Val)]

NM_007023.4(RAPGEF4):c.1546A>G (p.Ile516Val)

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.1546A>G (p.Ile516Val)

HGVS:

NC_000002.12:g.172996521A>G
NM_001100397.2:c.1114A>G
NM_001282899.2:c.1087A>G
NM_001282900.2:c.1033A>G
NM_001282901.2:c.886A>G
NM_001375864.1:c.1516A>G
NM_001375865.1:c.1546A>G
NM_001375866.1:c.1492A>G
NM_001375867.1:c.1453A>G
NM_001375868.1:c.1546A>G
NM_001375869.1:c.1546A>G
NM_001375870.1:c.1546A>G
NM_001375871.1:c.1492A>G
NM_001375872.1:c.1546A>G
NM_001375873.1:c.1492A>G
NM_001375874.1:c.1492A>G
NM_007023.4:c.1546A>GMANE SELECT
NP_001093867.1:p.Ile372Val
NP_001269828.1:p.Ile363Val
NP_001269829.1:p.Ile345Val
NP_001269830.1:p.Ile296Val
NP_001362793.1:p.Ile506Val
NP_001362794.1:p.Ile516Val
NP_001362795.1:p.Ile498Val
NP_001362796.1:p.Ile485Val
NP_001362797.1:p.Ile516Val
NP_001362798.1:p.Ile516Val
NP_001362799.1:p.Ile516Val
NP_001362800.1:p.Ile498Val
NP_001362801.1:p.Ile516Val
NP_001362802.1:p.Ile498Val
NP_001362803.1:p.Ile498Val
NP_008954.2:p.Ile516Val
NC_000002.11:g.173861249A>G
NM_007023.3:c.1546A>G
NR_164739.1:n.1685A>G
NR_164740.1:n.1631A>G
NR_164741.1:n.1631A>G

Protein change:

I296V

Links:

dbSNP: rs112722051

NCBI 1000 Genomes Browser:

rs112722051

Molecular consequence:

NM_001100397.2:c.1114A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282899.2:c.1087A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282900.2:c.1033A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282901.2:c.886A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375864.1:c.1516A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375865.1:c.1546A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375866.1:c.1492A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375867.1:c.1453A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375868.1:c.1546A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375869.1:c.1546A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375870.1:c.1546A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375871.1:c.1492A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375872.1:c.1546A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375873.1:c.1492A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375874.1:c.1492A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_007023.4:c.1546A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_164739.1:n.1685A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164740.1:n.1631A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164741.1:n.1631A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens tetratricopeptide repeat domain 9B, mRNA (cDNA clone MGC:33962 IMAGE:5303555), complete cds
gi|20810498|gb|BC029539.1|

Nucleotide
Luciobarbus numidiensis isolate NH25 control region and tRNA-Pro gene, complete ...
Luciobarbus numidiensis isolate NH25 control region and tRNA-Pro gene, complete sequence; and tRNA-Thr gene, partial sequence; mitochondrial
gi|1496234850|gb|MH187202.1|

Nucleotide
PREDICTED: Homo sapiens PTPRF interacting protein alpha 2 (PPFIA2), transcript v...
PREDICTED: Homo sapiens PTPRF interacting protein alpha 2 (PPFIA2), transcript variant X24, mRNA
gi|2462535297|ref|XM_054373667.1|

Nucleotide
Homo sapiens collagen, type IV, alpha 2, mRNA (cDNA clone IMAGE:5167975), with a...
Homo sapiens collagen, type IV, alpha 2, mRNA (cDNA clone IMAGE:5167975), with apparent retained intron
gi|23242347|gb|BC035559.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001120092	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jun 6, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005238418	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001120092

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jun 6, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005238418

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	not provided
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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001120092.1

#	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

From Breakthrough Genomics, Breakthrough Genomics, SCV005238418.1

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

#	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

Last Updated: Sep 29, 2024

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