NM_001375834.1(WIPF1):c.593C>T (p.Pro198Leu) AND not specified

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 24, 2024
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:: RCV000455771.6

Allele description [Variation Report for NM_001375834.1(WIPF1):c.593C>T (p.Pro198Leu)]

NM_001375834.1(WIPF1):c.593C>T (p.Pro198Leu)

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.593C>T (p.Pro198Leu)

HGVS:

NC_000002.12:g.174572212G>A
NG_032009.1:g.115688C>T
NM_001077269.1:c.593C>T
NM_001375832.1:c.593C>T
NM_001375833.1:c.593C>T
NM_001375834.1:c.593C>TMANE SELECT
NM_001375835.1:c.593C>T
NM_001375836.1:c.593C>T
NM_001375837.1:c.593C>T
NM_001375838.1:c.593C>T
NM_001375839.1:c.215C>T
NM_003387.5:c.593C>T
NP_001070737.1:p.Pro198Leu
NP_001362761.1:p.Pro198Leu
NP_001362762.1:p.Pro198Leu
NP_001362763.1:p.Pro198Leu
NP_001362764.1:p.Pro198Leu
NP_001362765.1:p.Pro198Leu
NP_001362766.1:p.Pro198Leu
NP_001362767.1:p.Pro198Leu
NP_001362768.1:p.Pro72Leu
NP_003378.3:p.Pro198Leu
LRG_374t1:c.593C>T
LRG_374:g.115688C>T
LRG_374p1:p.Pro198Leu
NC_000002.11:g.175436940G>A
NM_001375834.1:c.593C>T
NM_003387.4:c.593C>T

Protein change:

P198L

Links:

dbSNP: rs4972450

NCBI 1000 Genomes Browser:

rs4972450

Molecular consequence:

NM_001077269.1:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375832.1:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375833.1:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375834.1:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375835.1:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375836.1:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375837.1:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375838.1:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375839.1:c.215C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003387.5:c.593C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000540671	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Mar 28, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004234104	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jan 24, 2024)	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

SCV000540671

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Mar 28, 2016)

germline

clinical testing

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

SCV004234104

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jan 24, 2024)

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	no	88	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

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000540671.1

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

Description

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency

#	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 Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan, SCV004234104.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	88	not provided	not provided	clinical testing	PubMed (1)

Description

This variant is classified as Benign based on local population frequency. This variant was detected in 100% of patients studied by a panel of primary immunodeficiencies. Number of patients: 88. Only high quality variants are reported.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		88	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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