NM_007023.4(RAPGEF4):c.598T>A (p.Ser200Thr) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 5, 2023
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:: RCV004325221.1

Allele description [Variation Report for NM_007023.4(RAPGEF4):c.598T>A (p.Ser200Thr)]

NM_007023.4(RAPGEF4):c.598T>A (p.Ser200Thr)

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.598T>A (p.Ser200Thr)

HGVS:

NC_000002.12:g.172961128T>A
NM_001100397.2:c.166T>A
NM_001282899.2:c.139T>A
NM_001282900.2:c.85T>A
NM_001282901.2:c.-63T>A
NM_001375864.1:c.568T>A
NM_001375865.1:c.598T>A
NM_001375866.1:c.544T>A
NM_001375867.1:c.505T>A
NM_001375868.1:c.598T>A
NM_001375869.1:c.598T>A
NM_001375870.1:c.598T>A
NM_001375871.1:c.544T>A
NM_001375872.1:c.598T>A
NM_001375873.1:c.544T>A
NM_001375874.1:c.544T>A
NM_001375875.1:c.598T>A
NM_001375876.1:c.544T>A
NM_007023.4:c.598T>AMANE SELECT
NP_001093867.1:p.Ser56Thr
NP_001269828.1:p.Ser47Thr
NP_001269829.1:p.Ser29Thr
NP_001362793.1:p.Ser190Thr
NP_001362794.1:p.Ser200Thr
NP_001362795.1:p.Ser182Thr
NP_001362796.1:p.Ser169Thr
NP_001362797.1:p.Ser200Thr
NP_001362798.1:p.Ser200Thr
NP_001362799.1:p.Ser200Thr
NP_001362800.1:p.Ser182Thr
NP_001362801.1:p.Ser200Thr
NP_001362802.1:p.Ser182Thr
NP_001362803.1:p.Ser182Thr
NP_001362804.1:p.Ser200Thr
NP_001362805.1:p.Ser182Thr
NP_008954.2:p.Ser200Thr
NC_000002.11:g.173825856T>A
NM_007023.3:c.598T>A
NR_164739.1:n.737T>A
NR_164740.1:n.683T>A
NR_164741.1:n.683T>A

Protein change:

S169T

Molecular consequence:

NM_001282901.2:c.-63T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001100397.2:c.166T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282899.2:c.139T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282900.2:c.85T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375864.1:c.568T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375865.1:c.598T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375866.1:c.544T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375867.1:c.505T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375868.1:c.598T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375869.1:c.598T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375870.1:c.598T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375871.1:c.544T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375872.1:c.598T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375873.1:c.544T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375874.1:c.544T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375875.1:c.598T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375876.1:c.544T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_007023.4:c.598T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_164739.1:n.737T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164740.1:n.683T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164741.1:n.683T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Saccharomyces cerevisiae S288C uncharacterized protein (YHR219W), partial mRNA
Saccharomyces cerevisiae S288C uncharacterized protein (YHR219W), partial mRNA
gi|398365242|ref|NM_001179350.3|

Nucleotide
Homo sapiens ectodysplasin A receptor (EDAR), RefSeqGene on chromosome 2
Homo sapiens ectodysplasin A receptor (EDAR), RefSeqGene on chromosome 2
gi|194353941|ref|NG_008257.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003990205	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 5, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003990205

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 5, 2023)

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

Details of each submission

From Ambry Genetics, SCV003990205.2

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

Description

The c.598T>A (p.S200T) alteration is located in exon 8 (coding exon 8) of the RAPGEF4 gene. This alteration results from a T to A substitution at nucleotide position 598, causing the serine (S) at amino acid position 200 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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: Nov 10, 2024

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