NM_018124.4(RFWD3):c.1250C>G (p.Ser417Cys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 21, 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:: RCV003670458.2

Allele description [Variation Report for NM_018124.4(RFWD3):c.1250C>G (p.Ser417Cys)]

NM_018124.4(RFWD3):c.1250C>G (p.Ser417Cys)

Gene:

RFWD3:ring finger and WD repeat domain 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q23.1

Genomic location:

Preferred name:

NM_018124.4(RFWD3):c.1250C>G (p.Ser417Cys)

HGVS:

NC_000016.10:g.74636522G>C
NM_001370534.1:c.1250C>G
NM_001370535.1:c.1250C>G
NM_001370536.1:c.1250C>G
NM_001370537.1:c.416C>G
NM_001370539.1:c.416C>G
NM_001370540.1:c.416C>G
NM_001370541.1:c.416C>G
NM_001370542.1:c.416C>G
NM_001370543.1:c.416C>G
NM_018124.4:c.1250C>GMANE SELECT
NP_001357463.1:p.Ser417Cys
NP_001357464.1:p.Ser417Cys
NP_001357465.1:p.Ser417Cys
NP_001357466.1:p.Ser139Cys
NP_001357468.1:p.Ser139Cys
NP_001357469.1:p.Ser139Cys
NP_001357470.1:p.Ser139Cys
NP_001357471.1:p.Ser139Cys
NP_001357472.1:p.Ser139Cys
NP_060594.3:p.Ser417Cys
NC_000016.9:g.74670420G>C

Protein change:

S139C

Molecular consequence:

NM_001370534.1:c.1250C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370535.1:c.1250C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370536.1:c.1250C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370537.1:c.416C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370539.1:c.416C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370540.1:c.416C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370541.1:c.416C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370542.1:c.416C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370543.1:c.416C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_018124.4:c.1250C>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004389033	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 21, 2023)	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

SCV004389033

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 21, 2023)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004389033.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The cysteine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with RFWD3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 417 of the RFWD3 protein (p.Ser417Cys).

#	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: Sep 29, 2024

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