NM_018124.4(RFWD3):c.1223G>A (p.Ser408Asn) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 30, 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:: RCV003854709.2

Allele description [Variation Report for NM_018124.4(RFWD3):c.1223G>A (p.Ser408Asn)]

NM_018124.4(RFWD3):c.1223G>A (p.Ser408Asn)

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.1223G>A (p.Ser408Asn)

HGVS:

NC_000016.10:g.74636549C>T
NM_001370534.1:c.1223G>A
NM_001370535.1:c.1223G>A
NM_001370536.1:c.1223G>A
NM_001370537.1:c.389G>A
NM_001370539.1:c.389G>A
NM_001370540.1:c.389G>A
NM_001370541.1:c.389G>A
NM_001370542.1:c.389G>A
NM_001370543.1:c.389G>A
NM_018124.4:c.1223G>AMANE SELECT
NP_001357463.1:p.Ser408Asn
NP_001357464.1:p.Ser408Asn
NP_001357465.1:p.Ser408Asn
NP_001357466.1:p.Ser130Asn
NP_001357468.1:p.Ser130Asn
NP_001357469.1:p.Ser130Asn
NP_001357470.1:p.Ser130Asn
NP_001357471.1:p.Ser130Asn
NP_001357472.1:p.Ser130Asn
NP_060594.3:p.Ser408Asn
NC_000016.9:g.74670447C>T

Protein change:

S130N

Molecular consequence:

NM_001370534.1:c.1223G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370535.1:c.1223G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370536.1:c.1223G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370537.1:c.389G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370539.1:c.389G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370540.1:c.389G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370541.1:c.389G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370542.1:c.389G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370543.1:c.389G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_018124.4:c.1223G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Gene Links for GEO Profiles (Select 103984493) (1)
Gene
As3mt arsenite methyltransferase [Rattus norvegicus]
As3mt arsenite methyltransferase [Rattus norvegicus]
Gene ID:140925

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004660314	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 30, 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

SCV004660314

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 30, 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, SCV004660314.1

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

Description

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 asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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. This variant has not been reported in the literature in individuals affected with RFWD3-related conditions. This variant is present in population databases (rs766228902, gnomAD 0.003%). This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 408 of the RFWD3 protein (p.Ser408Asn).

#	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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