NM_025132.4(WDR19):c.233G>A (p.Cys78Tyr) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 17, 2022
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:: RCV001996873.3

Allele description

NM_025132.4(WDR19):c.233G>A (p.Cys78Tyr)

Gene:

WDR19:WD repeat domain 19 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p14

Genomic location:

Preferred name:

NM_025132.4(WDR19):c.233G>A (p.Cys78Tyr)

HGVS:

NC_000004.12:g.39189724G>A
NG_031813.1:g.12321G>A
NM_001317924.2:c.-132G>A
NM_025132.4:c.233G>AMANE SELECT
NP_079408.3:p.Cys78Tyr
NC_000004.11:g.39191344G>A

Protein change:

C78Y

Links:

dbSNP: rs200354828

NCBI 1000 Genomes Browser:

rs200354828

Molecular consequence:

NM_001317924.2:c.-132G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_025132.4:c.233G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Asphyxiating thoracic dystrophy 5 (SRTD5)
Synonyms:: SHORT-RIB THORACIC DYSPLASIA 5 WITH OR WITHOUT POLYDACTYLY; SHORT-RIB THORACIC DYSPLASIA 5 WITHOUT POLYDACTYLY
Identifiers:: MONDO: MONDO:0013717; MedGen: C3280598; Orphanet: 474; OMIM: 614376

Name:: Senior-Loken syndrome 8 (SLSN8)
Identifiers:: MONDO: MONDO:0014579; MedGen: C4225376; Orphanet: 3156; OMIM: 616307

Recent activity

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dof zinc finger protein DOF2.1 [Solanum lycopersicum]
dof zinc finger protein DOF2.1 [Solanum lycopersicum]
gi|460391308|ref|XP_004241265.1|

Protein
dof zinc finger protein DOF3.4 [Solanum lycopersicum]
dof zinc finger protein DOF3.4 [Solanum lycopersicum]
gi|460372500|ref|XP_004232067.1|

Protein
cyclic dof factor 1 [Solanum lycopersicum]
cyclic dof factor 1 [Solanum lycopersicum]
gi|460380496|ref|XP_004235992.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002220213	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 17, 2022)	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

SCV002220213

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 17, 2022)

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 Invitae, SCV002220213.3

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

Description

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. 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: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with WDR19-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 78 of the WDR19 protein (p.Cys78Tyr).

#	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: Feb 28, 2024

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