NM_003394.4(WNT10B):c.338-1G>C AND Split hand-foot malformation 6

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Mar 17, 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:: RCV000656339.6

Allele description [Variation Report for NM_003394.4(WNT10B):c.338-1G>C]

NM_003394.4(WNT10B):c.338-1G>C

Gene:

WNT10B:Wnt family member 10B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.12

Genomic location:

Preferred name:

NM_003394.4(WNT10B):c.338-1G>C

HGVS:

NC_000012.12:g.48968320C>G
NG_023347.1:g.8539G>C
NG_125611.1:g.811C>G
NM_003394.4:c.338-1G>CMANE SELECT
NC_000012.11:g.49362103C>G
NM_003394.3:c.338-1G>C

Links:

dbSNP: rs1163162816

NCBI 1000 Genomes Browser:

rs1163162816

Molecular consequence:

NM_003394.4:c.338-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

Functional consequence:

effect on transcription [Variation Ontology: 0149]

Observations:

Condition(s)

Name:: Split hand-foot malformation 6
Synonyms:: ECTRODACTYLY, AUTOSOMAL RECESSIVE; Split-hand/foot malformation 6
Identifiers:: MONDO: MONDO:0009157; MedGen: C2749665; Orphanet: 2440; OMIM: 225300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000778302	Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	no assertion criteria provided	Likely pathogenic (Dec 5, 2017)	germline	clinical testing
SCV000925757	Molecular Pathology and Genetics, King Abdulaziz Medical City, Ministry of National Guard - Health Affairs	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 30, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001522970	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 17, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004805144	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 17, 2024)	germline	research	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	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	research
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
Saudi	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City, SCV000778302.1

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

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

From Molecular Pathology and Genetics, King Abdulaziz Medical City, Ministry of National Guard - Health Affairs, SCV000925757.1

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

Description

NGS panel, confirmed by sanger and qn RT-PCR gene expression

Description

More clinical presentation will be seen in accepted publication for Al Ghamdi et al. 2019.

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

From Baylor Genetics, SCV001522970.1

#	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 pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	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, SCV004805144.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	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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