NM_001375834.1(WIPF1):c.851CTC[3] (p.Pro287del) AND Wiskott-Aldrich syndrome 2

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 4, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000814777.6

Allele description [Variation Report for NM_001375834.1(WIPF1):c.851CTC[3] (p.Pro287del)]

NM_001375834.1(WIPF1):c.851CTC[3] (p.Pro287del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

2q31.1

Genomic location:

Preferred name:

NM_001375834.1(WIPF1):c.851CTC[3] (p.Pro287del)

HGVS:

NC_000002.12:g.174571944AGG[3]
NG_032009.1:g.115946CTC[3]
NM_001077269.1:c.851CTC[3]
NM_001077269.1:c.860_862del
NM_001375832.1:c.851CTC[3]
NM_001375833.1:c.851CTC[3]
NM_001375834.1:c.851CTC[3]MANE SELECT
NM_001375835.1:c.851CTC[3]
NM_001375836.1:c.851CTC[3]
NM_001375837.1:c.851CTC[3]
NM_001375838.1:c.851CTC[3]
NM_001375839.1:c.473CTC[3]
NM_003387.5:c.851CTC[3]
NP_001070737.1:p.Pro287del
NP_001362761.1:p.Pro287del
NP_001362762.1:p.Pro287del
NP_001362763.1:p.Pro287del
NP_001362764.1:p.Pro287del
NP_001362765.1:p.Pro287del
NP_001362766.1:p.Pro287del
NP_001362767.1:p.Pro287del
NP_001362768.1:p.Pro161del
NP_003378.3:p.Pro287del
LRG_374t1:c.851CTC[3]
LRG_374:g.115946CTC[3]
LRG_374p1:p.Pro287del
NC_000002.11:g.175436671_175436673del
NC_000002.11:g.175436672AGG[3]
NM_001077269.1:c.860_862del
NM_001077269.1:c.860_862delCTC

Protein change:

P161del

Links:

dbSNP: rs556678311

NCBI 1000 Genomes Browser:

rs556678311

Molecular consequence:

NM_001077269.1:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001375832.1:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001375833.1:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001375834.1:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001375835.1:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001375836.1:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001375837.1:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001375838.1:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001375839.1:c.473CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_003387.5:c.851CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000955202	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 4, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001528787	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 3, 2018)	maternal	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

SCV000955202

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 4, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001528787

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 3, 2018)

maternal

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	maternal	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000955202.4

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

Description

This variant, c.860_862del, results in the deletion of 1 amino acid(s) of the WIPF1 protein (p.Pro287del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with WIPF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 658041). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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

From Baylor Genetics, SCV001528787.1

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

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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