NC_000005.9:g.(?_176047812)_(177422934_?)del AND Ehlers-Danlos syndrome progeroid type

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 21, 2021
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:: RCV001931790.4

Allele description [Variation Report for NC_000005.9:g.(?_176047812)_(177422934_?)del]

NC_000005.9:g.(?_176047812)_(177422934_?)del

Genes:

DDX41:DEAD-box helicase 41 [Gene - OMIM - HGNC]
GRK6:G protein-coupled receptor kinase 6 [Gene - OMIM - HGNC]
MXD3:MAX dimerization protein 3 [Gene - OMIM - HGNC]
PDLIM7:PDZ and LIM domain 7 [Gene - OMIM - HGNC]
PRELID1:PRELI domain containing 1 [Gene - OMIM - HGNC]
PROP1:PROP paired-like homeobox 1 [Gene - OMIM - HGNC]
RAB24:RAB24, member RAS oncogene family [Gene - OMIM - HGNC]
B4GALT7:beta-1,4-galactosyltransferase 7 [Gene - OMIM - HGNC]
F12:coagulation factor XII [Gene - OMIM - HGNC]
DOK3:docking protein 3 [Gene - OMIM - HGNC]
DBN1:drebrin 1 [Gene - OMIM - HGNC]
EIF4E1B:eukaryotic translation initiation factor 4E family member 1B [Gene - HGNC]
FAM153A:family with sequence similarity 153 member A [Gene - HGNC]
FAM193B:family with sequence similarity 193 member B [Gene - OMIM - HGNC]
FGFR4:fibroblast growth factor receptor 4 [Gene - OMIM - HGNC]
HK3:hexokinase 3 [Gene - OMIM - HGNC]
LMAN2:lectin, mannose binding 2 [Gene - OMIM - HGNC]
NSD1:nuclear receptor binding SET domain protein 1 [Gene - OMIM - HGNC]
PFN3:profilin 3 [Gene - OMIM - HGNC]
PRR7:proline rich 7, synaptic [Gene - OMIM - HGNC]
RGS14:regulator of G protein signaling 14 [Gene - OMIM - HGNC]
SLC34A1:solute carrier family 34 member 1 [Gene - OMIM - HGNC]
SNCB:synuclein beta [Gene - OMIM - HGNC]
TSPAN17:tetraspanin 17 [Gene - OMIM - HGNC]
TMED9:transmembrane p24 trafficking protein 9 [Gene - OMIM - HGNC]
UIMC1:ubiquitin interaction motif containing 1 [Gene - OMIM - HGNC]
UNC5A:unc-5 netrin receptor A [Gene - OMIM - HGNC]
ZNF346:zinc finger protein 346 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q35.2-35.3

Genomic location:

Chr5: 176047812 - 177422934 (on Assembly GRCh37)

Preferred name:

NC_000005.9:g.(?_176047812)_(177422934_?)del

HGVS:

NC_000005.9:g.(?_176047812)_(177422934_?)del

Condition(s)

Name:: Ehlers-Danlos syndrome progeroid type
Synonyms:: Ehlers-Danlos syndrome, spondylodysplastic type
Identifiers:: MONDO: MONDO:0007526; MedGen: CN030853; Orphanet: 75496

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002210586	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 21, 2021)	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

SCV002210586

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 21, 2021)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002210586.3

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the B4GALT7 gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in B4GALT7 cause disease. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with B4GALT7-related conditions. 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.

#	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: Dec 17, 2023

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