NC_000009.11:g.(?_134379574)_(138678377_?)dup AND Ehlers-Danlos syndrome, classic type

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 17, 2018
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:: RCV000807925.3

Allele description

NC_000009.11:g.(?_134379574)_(138678377_?)dup

Genes:

ABO:ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase [Gene - OMIM - HGNC]
ADAMTS13:ADAM metallopeptidase with thrombospondin type 1 motif 13 [Gene - OMIM - HGNC]
ADAMTSL2:ADAMTS like 2 [Gene - OMIM - HGNC]
BARHL1:BarH like homeobox 1 [Gene - OMIM - HGNC]
DDX31:DEAD-box helicase 31 [Gene - OMIM - HGNC]
REXO4:REX4 homolog, 3'-5' exonuclease [Gene - OMIM - HGNC]
RNU6ATAC:RNA, U6atac small nuclear [Gene - OMIM - HGNC]
RAPGEF1:Rap guanine nucleotide exchange factor 1 [Gene - OMIM - HGNC]
SURF1:SURF1 cytochrome c oxidase assembly factor [Gene - OMIM - HGNC]
TSC1:TSC complex subunit 1 [Gene - OMIM - HGNC]
WDR5:WD repeat domain 5 [Gene - OMIM - HGNC]
AK8:adenylate kinase 8 [Gene - OMIM - HGNC]
BRD3:bromodomain containing 3 [Gene - OMIM - HGNC]
CACFD1:calcium channel flower domain containing 1 [Gene - OMIM - HGNC]
CEL:carboxyl ester lipase [Gene - OMIM - HGNC]
CFAP77:cilia and flagella associated protein 77 [Gene - HGNC]
COL5A1:collagen type V alpha 1 chain [Gene - OMIM - HGNC]
DBH:dopamine beta-hydroxylase [Gene - OMIM - HGNC]
FAM163B:family with sequence similarity 163 member B [Gene - HGNC]
FCN1:ficolin 1 [Gene - OMIM - HGNC]
FCN2:ficolin 2 [Gene - OMIM - HGNC]
GTF3C4:general transcription factor IIIC subunit 4 [Gene - OMIM - HGNC]
GTF3C5:general transcription factor IIIC subunit 5 [Gene - OMIM - HGNC]
GBGT1:globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group) [Gene - OMIM - HGNC]
GLT6D1:glycosyltransferase 6 domain containing 1 [Gene - OMIM - HGNC]
GFI1B:growth factor independent 1B transcriptional repressor [Gene - OMIM - HGNC]
LCN1:lipocalin 1 [Gene - OMIM - HGNC]
LCN9:lipocalin 9 [Gene - OMIM - HGNC]
LINC02907:long intergenic non-protein coding RNA 2907 [Gene - HGNC]
MED22:mediator complex subunit 22 [Gene - OMIM - HGNC]
MED27:mediator complex subunit 27 [Gene - OMIM - HGNC]
MRPS2:mitochondrial ribosomal protein S2 [Gene - OMIM - HGNC]
MYMK:myomaker, myoblast fusion factor [Gene - OMIM - HGNC]
NTNG2:netrin G2 [Gene - OMIM - HGNC]
OBP2A:odorant binding protein 2A [Gene - OMIM - HGNC]
OBP2B:odorant binding protein 2B [Gene - OMIM - HGNC]
OLFM1:olfactomedin 1 [Gene - OMIM - HGNC]
PIERCE1:piercer of microtubule wall 1 [Gene - OMIM - HGNC]
KCNT1:potassium sodium-activated channel subfamily T member 1 [Gene - OMIM - HGNC]
PAEP:progestagen associated endometrial protein [Gene - OMIM - HGNC]
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
PPP1R26:protein phosphatase 1 regulatory subunit 26 [Gene - OMIM - HGNC]
RALGDS:ral guanine nucleotide dissociation stimulator [Gene - OMIM - HGNC]
RXRA:retinoid X receptor alpha [Gene - OMIM - HGNC]
RPL7A:ribosomal protein L7a [Gene - OMIM - HGNC]
SARDH:sarcosine dehydrogenase [Gene - OMIM - HGNC]
SETX:senataxin [Gene - OMIM - HGNC]
STKLD1:serine/threonine kinase like domain containing 1 [Gene - OMIM - HGNC]
SLC2A6:solute carrier family 2 member 6 [Gene - OMIM - HGNC]
SPACA9:sperm acrosome associated 9 [Gene - OMIM - HGNC]
SOHLH1:spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Gene - OMIM - HGNC]
SURF2:surfeit 2 [Gene - OMIM - HGNC]
SURF4:surfeit 4 [Gene - OMIM - HGNC]
SURF6:surfeit 6 [Gene - OMIM - HGNC]
TTF1:transcription termination factor 1 [Gene - OMIM - HGNC]
UCK1:uridine-cytidine kinase 1 [Gene - OMIM - HGNC]
VAV2:vav guanine nucleotide exchange factor 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

9q34.13-34.3

Genomic location:

Chr9: 134379574 - 138678377 (on Assembly GRCh37)

Preferred name:

NC_000009.11:g.(?_134379574)_(138678377_?)dup

HGVS:

NC_000009.11:g.(?_134379574)_(138678377_?)dup

Condition(s)

Name:: Ehlers-Danlos syndrome, classic type (cEDS)
Identifiers:: MONDO: MONDO:0007522; MedGen: C4225429; Orphanet: 287

Recent activity

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SAMN33745800 (1)
SRA
tRNA (32-2'-O)-methyltransferase regulator THADA isoform X1 [Rattus norvegicus]
tRNA (32-2'-O)-methyltransferase regulator THADA isoform X1 [Rattus norvegicus]
gi|2678951199|ref|XP_063117898.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000948005	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 17, 2018)	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

SCV000948005

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 17, 2018)

germline

clinical testing

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	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, SCV000948005.1

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the COL5A1 gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals with COL5A1-related disease. 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: Mar 26, 2023

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