NC_000005.9:g.(?_178554940)_(178555139_?)del AND Ehlers-Danlos syndrome, dermatosparaxis type

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 31, 2023
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:: RCV004579016.2

Allele description [Variation Report for NC_000005.9:g.(?_178554940)_(178555139_?)del]

NC_000005.9:g.(?_178554940)_(178555139_?)del

Gene:: ADAMTS2:ADAM metallopeptidase with thrombospondin type 1 motif 2 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 5q35.3
Genomic location:: Chr5: 178554940 - 178555139 (on Assembly GRCh37)
Preferred name:: NC_000005.9:g.(?_178554940)_(178555139_?)del
HGVS:: NC_000005.9:g.(?_178554940)_(178555139_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Ehlers-Danlos syndrome, dermatosparaxis type
Synonyms:: EDS VIIC; Dermatosparaxis; Ehlers-Danlos syndrome type 7C (formerly); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009161; MedGen: C2700425; Orphanet: 1901; OMIM: 225410

Recent activity

Clear Turn Off Turn On

Heliconia x rauliniana voucher Abalo sn A 18S ribosomal RNA gene, partial sequen...
Heliconia x rauliniana voucher Abalo sn A 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 26S ribosomal RNA gene, partial sequence
gi|1237077889|gb|KY215132.1|

Nucleotide
zinc finger protein 418 isoform X6 [Homo sapiens]
zinc finger protein 418 isoform X6 [Homo sapiens]
gi|2217319361|ref|XP_047294170.1|

Protein
PREDICTED: Homo sapiens zinc finger protein 418 (ZNF418), transcript variant X5,...
PREDICTED: Homo sapiens zinc finger protein 418 (ZNF418), transcript variant X5, mRNA
gi|2217319324|ref|XM_047438197.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005063007	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 31, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 10417273, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005063007

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 31, 2023)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Human Ehlers-Danlos syndrome type VII C and bovine dermatosparaxis are caused by mutations in the procollagen I N-proteinase gene.

Colige A, Sieron AL, Li SW, Schwarze U, Petty E, Wertelecki W, Wilcox W, Krakow D, Cohn DH, Reardon W, Byers PH, Lapière CM, Prockop DJ, Nusgens BV.

Am J Hum Genet. 1999 Aug;65(2):308-17.

PubMed [citation]

PMID:: 10417273
PMCID:: PMC1377929

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV005063007.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 17 of the ADAMTS2 gene. This deletion is out-of-frame, and is expected to create a premature termination codon and result in an absent or disrupted protein product. Loss-of-function variants in ADAMTS2 are known to be pathogenic (PMID: 10417273). This variant has not been reported in the literature in individuals affected with ADAMTS2-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine