NC_000011.9:g.(?_117856768)_(118972385_?)del AND Inflammatory bowel disease 28

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 7, 2019
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:: RCV001386823.3

Allele description

NC_000011.9:g.(?_117856768)_(118972385_?)del

Genes:

ATP5MG:ATP synthase membrane subunit g [Gene - OMIM - HGNC]
BCL9L:BCL9 like [Gene - OMIM - HGNC]
CXCR5:C-X-C motif chemokine receptor 5 [Gene - OMIM - HGNC]
CD3D:CD3 delta subunit of T-cell receptor complex [Gene - OMIM - HGNC]
CD3E:CD3 epsilon subunit of T-cell receptor complex [Gene - OMIM - HGNC]
CD3G:CD3 gamma subunit of T-cell receptor complex [Gene - OMIM - HGNC]
DDX6:DEAD-box helicase 6 [Gene - OMIM - HGNC]
H2AX:H2A.X variant histone [Gene - OMIM - HGNC]
VPS11:VPS11 core subunit of CORVET and HOPS complexes [Gene - OMIM - HGNC]
ARCN1:archain 1 [Gene - OMIM - HGNC]
CENATAC:centrosomal AT-AC splicing factor [Gene - OMIM - HGNC]
DPAGT1:dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 [Gene - OMIM - HGNC]
FOXR1:forkhead box R1 [Gene - OMIM - HGNC]
HMBS:hydroxymethylbilane synthase [Gene - OMIM - HGNC]
HYOU1:hypoxia up-regulated 1 [Gene - OMIM - HGNC]
IL10RA:interleukin 10 receptor subunit alpha [Gene - OMIM - HGNC]
IFT46:intraflagellar transport 46 [Gene - HGNC]
JAML:junction adhesion molecule like [Gene - OMIM - HGNC]
KMT2A:lysine methyltransferase 2A [Gene - OMIM - HGNC]
MPZL2:myelin protein zero like 2 [Gene - OMIM - HGNC]
MPZL3:myelin protein zero like 3 [Gene - OMIM - HGNC]
PHLDB1:pleckstrin homology like domain family B member 1 [Gene - OMIM - HGNC]
RPS25:ribosomal protein S25 [Gene - OMIM - HGNC]
SCN2B:sodium voltage-gated channel beta subunit 2 [Gene - OMIM - HGNC]
SCN4B:sodium voltage-gated channel beta subunit 4 [Gene - OMIM - HGNC]
SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]
TTC36:tetratricopeptide repeat domain 36 [Gene - HGNC]
TRAPPC4:trafficking protein particle complex subunit 4 [Gene - OMIM - HGNC]
TMEM25:transmembrane protein 25 [Gene - OMIM - HGNC]
TMPRSS4:transmembrane serine protease 4 [Gene - OMIM - HGNC]
TREH:trehalase [Gene - OMIM - HGNC]
UBE4A:ubiquitination factor E4A [Gene - OMIM - HGNC]
UPK2:uroplakin 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q23.3

Genomic location:

Chr11: 117856768 - 118972385 (on Assembly GRCh37)

Preferred name:

NC_000011.9:g.(?_117856768)_(118972385_?)del

HGVS:

NC_000011.9:g.(?_117856768)_(118972385_?)del

Condition(s)

Name:: Inflammatory bowel disease 28
Synonyms:: Inflammatory bowel disease 28, autosomal recessive; Inflammatory bowel disease 28, early onset, autosomal recessive
Identifiers:: MONDO: MONDO:0013153; MedGen: C2751053; Orphanet: 238569; OMIM: 613148

Recent activity

Clear Turn Off Turn On

Glucose-6-phosphate transport defect
Glucose-6-phosphate transport defect

MedGen
C0268146[conceptid] (1)
MedGen

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
SCV001587182	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 7, 2019)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 24216686, 25373860, 26822028, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001587182

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 7, 2019)

germline

clinical testing

PubMed (4)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Phenotypic characterization of very early-onset IBD due to mutations in the IL10, IL10 receptor alpha or beta gene: a survey of the Genius Working Group.

Pigneur B, Escher J, Elawad M, Lima R, Buderus S, Kierkus J, Guariso G, Canioni D, Lambot K, Talbotec C, Shah N, Begue B, Rieux-Laucat F, Goulet O, Cerf-Bensussan N, Neven B, Ruemmele FM.

Inflamm Bowel Dis. 2013 Dec;19(13):2820-8. doi: 10.1097/01.MIB.0000435439.22484.d3.

PubMed [citation]

PMID:: 24216686

Clinical features of interleukin 10 receptor gene mutations in children with very early-onset inflammatory bowel disease.

Beser OF, Conde CD, Serwas NK, Cokugras FC, Kutlu T, Boztug K, Erkan T.

J Pediatr Gastroenterol Nutr. 2015 Mar;60(3):332-8. doi: 10.1097/MPG.0000000000000621.

PubMed [citation]

PMID:: 25373860

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001587182.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the IL10RA gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with IL10RA-related conditions. Loss-of-function variants in IL10RA are known to be pathogenic (PMID: 24216686, 25373860, 26822028). 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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 13, 2023

ClinVar

Relating variation to medicine