NM_001375834.1(WIPF1):c.532T>A (p.Ser178Thr) AND Wiskott-Aldrich syndrome 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 12, 2021
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:: RCV002726454.3

Allele description [Variation Report for NM_001375834.1(WIPF1):c.532T>A (p.Ser178Thr)]

NM_001375834.1(WIPF1):c.532T>A (p.Ser178Thr)

Gene:

WIPF1:WAS/WASL interacting protein family member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.1

Genomic location:

Preferred name:

NM_001375834.1(WIPF1):c.532T>A (p.Ser178Thr)

HGVS:

NC_000002.12:g.174572273A>T
NG_032009.1:g.115627T>A
NM_001077269.1:c.532T>A
NM_001375832.1:c.532T>A
NM_001375833.1:c.532T>A
NM_001375834.1:c.532T>AMANE SELECT
NM_001375835.1:c.532T>A
NM_001375836.1:c.532T>A
NM_001375837.1:c.532T>A
NM_001375838.1:c.532T>A
NM_001375839.1:c.182-28T>A
NM_003387.5:c.532T>A
NP_001070737.1:p.Ser178Thr
NP_001362761.1:p.Ser178Thr
NP_001362762.1:p.Ser178Thr
NP_001362763.1:p.Ser178Thr
NP_001362764.1:p.Ser178Thr
NP_001362765.1:p.Ser178Thr
NP_001362766.1:p.Ser178Thr
NP_001362767.1:p.Ser178Thr
NP_003378.3:p.Ser178Thr
LRG_374t1:c.532T>A
LRG_374:g.115627T>A
LRG_374p1:p.Ser178Thr
NC_000002.11:g.175437001A>T

Protein change:

S178T

Molecular consequence:

NM_001375839.1:c.182-28T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001077269.1:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375832.1:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375833.1:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375834.1:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375835.1:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375836.1:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375837.1:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375838.1:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003387.5:c.532T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Wiskott-Aldrich syndrome 2 (WAS2)
Synonyms:: WIPF1 DEFICIENCY
Identifiers:: MONDO: MONDO:0013779; MedGen: C3281001; Orphanet: 906; OMIM: 614493

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003004905	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 12, 2021)	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

SCV003004905

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 12, 2021)

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, SCV003004905.2

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

Description

This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 178 of the WIPF1 protein (p.Ser178Thr). This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with WIPF1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). 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.

#	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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