NM_001375834.1(WIPF1):c.587C>G (p.Ser196Ter) AND Wiskott-Aldrich syndrome 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 6, 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:: RCV003643830.2

Allele description [Variation Report for NM_001375834.1(WIPF1):c.587C>G (p.Ser196Ter)]

NM_001375834.1(WIPF1):c.587C>G (p.Ser196Ter)

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.587C>G (p.Ser196Ter)

HGVS:

NC_000002.12:g.174572218G>C
NG_032009.1:g.115682C>G
NM_001077269.1:c.587C>G
NM_001375832.1:c.587C>G
NM_001375833.1:c.587C>G
NM_001375834.1:c.587C>GMANE SELECT
NM_001375835.1:c.587C>G
NM_001375836.1:c.587C>G
NM_001375837.1:c.587C>G
NM_001375838.1:c.587C>G
NM_001375839.1:c.209C>G
NM_003387.5:c.587C>G
NP_001070737.1:p.Ser196Ter
NP_001362761.1:p.Ser196Ter
NP_001362762.1:p.Ser196Ter
NP_001362763.1:p.Ser196Ter
NP_001362764.1:p.Ser196Ter
NP_001362765.1:p.Ser196Ter
NP_001362766.1:p.Ser196Ter
NP_001362767.1:p.Ser196Ter
NP_001362768.1:p.Ser70Ter
NP_003378.3:p.Ser196Ter
LRG_374t1:c.587C>G
LRG_374:g.115682C>G
LRG_374p1:p.Ser196Ter
NC_000002.11:g.175436946G>C

Protein change:

S196*

Molecular consequence:

NM_001077269.1:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001375832.1:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001375833.1:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001375834.1:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001375835.1:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001375836.1:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001375837.1:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001375838.1:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001375839.1:c.209C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_003387.5:c.587C>G - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004490626	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 6, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22231303, 27742395, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004490626

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 6, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

A novel primary human immunodeficiency due to deficiency in the WASP-interacting protein WIP.

Lanzi G, Moratto D, Vairo D, Masneri S, Delmonte O, Paganini T, Parolini S, Tabellini G, Mazza C, Savoldi G, Montin D, Martino S, Tovo P, Pessach IM, Massaad MJ, Ramesh N, Porta F, Plebani A, Notarangelo LD, Geha RS, Giliani S.

J Exp Med. 2012 Jan 16;209(1):29-34. doi: 10.1084/jem.20110896. Epub 2012 Jan 9.

PubMed [citation]

PMID:: 22231303
PMCID:: PMC3260865

Hematopoietic stem cell transplantation corrects WIP deficiency.

Al-Mousa H, Hawwari A, Al-Ghonaium A, Al-Saud B, Al-Dhekri H, Al-Muhsen S, Elshorbagi S, Dasouki M, El-Baik L, Alseraihy A, Ayas M, Arnaout R.

J Allergy Clin Immunol. 2017 Mar;139(3):1039-1040.e4. doi: 10.1016/j.jaci.2016.08.036. Epub 2016 Oct 11. No abstract available.

PubMed [citation]

PMID:: 27742395

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004490626.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with WIPF1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser196*) in the WIPF1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in WIPF1 are known to be pathogenic (PMID: 22231303, 27742395).

#	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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