NM_004625.4(WNT7A):c.874C>T (p.Arg292Cys) AND Schinzel phocomelia syndrome

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 25, 2024
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:: RCV000008526.5

Allele description [Variation Report for NM_004625.4(WNT7A):c.874C>T (p.Arg292Cys)]

NM_004625.4(WNT7A):c.874C>T (p.Arg292Cys)

Gene:

WNT7A:Wnt family member 7A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_004625.4(WNT7A):c.874C>T (p.Arg292Cys)

HGVS:

NC_000003.12:g.13819120G>A
NG_008088.1:g.66002C>T
NM_004625.3:c.874C>T
NM_004625.4:c.874C>TMANE SELECT
NP_004616.2:p.Arg292Cys
NC_000003.11:g.13860617G>A
O00755:p.Arg292Cys

Protein change:

R292C; ARG292CYS

Links:

UniProtKB: O00755#VAR_030674; OMIM: 601570.0001; dbSNP: rs104893835

NCBI 1000 Genomes Browser:

rs104893835

Molecular consequence:

NM_004625.4:c.874C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Schinzel phocomelia syndrome
Synonyms:: AL-AWADI/RAAS-ROTHSCHILD SYNDROME; LIMB/PELVIS-HYPOPLASIA/APLASIA SYNDROME; Al-Awadi/Raas-Rothschild/Schinzel phocomelia syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010164; MedGen: C1848651; Orphanet: 2879; OMIM: 276820

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Lactobacillus johnsonii strain N5 chromosome, complete genome
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000028734	OMIM	no assertion criteria provided	Pathogenic (Aug 1, 2006)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV004806262	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 25, 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

SCV000028734

OMIM

no assertion criteria provided

Pathogenic
(Aug 1, 2006)

germline

literature only

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

SCV004806262

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 25, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Mutations in WNT7A cause a range of limb malformations, including Fuhrmann syndrome and Al-Awadi/Raas-Rothschild/Schinzel phocomelia syndrome.

Woods CG, Stricker S, Seemann P, Stern R, Cox J, Sherridan E, Roberts E, Springell K, Scott S, Karbani G, Sharif SM, Toomes C, Bond J, Kumar D, Al-Gazali L, Mundlos S.

Am J Hum Genet. 2006 Aug;79(2):402-8. Epub 2006 Jun 23.

PubMed [citation]

PMID:: 16826533
PMCID:: PMC1559483

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 OMIM, SCV000028734.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

Woods et al. (2006) demonstrated a homozygous missense mutation in the WNT7A gene, arg292 to cys (R292C), in a consanguineous family in which 3 members had absent ulna and fibula with severe limb deficiency (276820), also known as Al-Awadi/Raas-Rothschild/Schinzel phocomelia syndrome. The R292C mutation arose from an 1179C-T transition in exon 4.

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

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004806262.1

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

#	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: Aug 4, 2024

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