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Gene: CHKB-DT (CHKB divergent transcript) Homo sapiens

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Symbol:

CHKB-DT

Name:

CHKB divergent transcript

RGD ID:

7254767

HGNC Page

HGNC:40146

Description:

ASSOCIATED WITH chromosome 22q13 duplication syndrome; Phelan-McDermid syndrome; INTERACTS WITH aflatoxin B1; cisplatin; methotrexate

Type:

ncrna (Ensembl: lncRNA)

RefSeq Status:

VALIDATED

Previously known as:

CHKB antisense RNA 1 (head to head); CHKB-AS1; HRAT

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	22	50,583,026 - 50,595,281 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	22	50,583,026 - 50,597,599 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	22	51,021,455 - 51,033,710 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Celera	22	34,897,488 - 34,898,389 (+)	NCBI		Celera
Cytogenetic Map	22	q13.33	NCBI
HuRef	22	33,912,454 - 33,913,355 (+)	NCBI		HuRef
CHM1_1	22	50,980,188 - 50,981,089 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	22	51,093,554 - 51,105,799 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
CHKB-DT	Human	chromosome 22q13 duplication syndrome		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Chromosome 22q13 duplication syndrome	ClinVar	PMID:31690835
CHKB-DT	Human	Phelan-McDermid syndrome		IAGP	(Homo sapiens) more ...	8554872	ClinVar Annotator: match by term: Phelan-McDermid syndrome	ClinVar

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
CHKB-DT	Human	aflatoxin B1	increases methylation	EXP		6480464	Aflatoxin B1 results in increased methylation of CHKB-DT gene	CTD	PMID:27153756
CHKB-DT	Human	cisplatin	multiple interactions	EXP		6480464	[Cisplatin co-treated with jinfukang] results in increased expression of CHKB-DT mRNA	CTD	PMID:27392435
CHKB-DT	Human	methotrexate	decreases expression	EXP		6480464	Methotrexate results in decreased expression of CHKB-DT mRNA	CTD	PMID:24449571
CHKB-DT	Human	valproic acid	increases methylation	EXP		6480464	Valproic Acid results in increased methylation of CHKB-DT gene	CTD	PMID:29154799

#	Reference Title	Reference Citation
1.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

PMID:15461802	PMID:36172578

Variants in CHKB-DT
7 total Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3	copy number gain	See cases [RCV000133646]	Chr22:16916608..50739836 [GRCh38] Chr22:17397498..51178264 [GRCh37] Chr22:15777498..49525130 [NCBI36] Chr22:22q11.1-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:49378128-50739836)x1	copy number loss	See cases [RCV000133859]	Chr22:49378128..50739836 [GRCh38] Chr22:49774048..51178264 [GRCh37] Chr22:48160052..49525130 [NCBI36] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:44606363-50739836)x1	copy number loss	See cases [RCV000133865]	Chr22:44606363..50739836 [GRCh38] Chr22:45002243..51178264 [GRCh37] Chr22:43380907..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
NR_110536.1(CHKB-AS1):n.594+20G>A	single nucleotide variant	Lung cancer [RCV000102116]	Chr22:50587475 [GRCh38] Chr22:51025904 [GRCh37] Chr22:22q13.33	uncertain significance
GRCh38/hg38 22q13.33(chr22:49315518-50739836)x1	copy number loss	See cases [RCV000133707]	Chr22:49315518..50739836 [GRCh38] Chr22:49711443..51178264 [GRCh37] Chr22:48097447..49525130 [NCBI36] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3	copy number gain	See cases [RCV000134730]	Chr22:16916743..50739785 [GRCh38] Chr22:17397633..51178213 [GRCh37] Chr22:15777633..49525079 [NCBI36] Chr22:22q11.1-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:49504768-50780581)x1	copy number loss	See cases [RCV000135691]	Chr22:49504768..50780581 [GRCh38] Chr22:49898417..51203353 [GRCh37] Chr22:48284421..49565875 [NCBI36] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43902561-50739836)x1	copy number loss	See cases [RCV000135444]	Chr22:43902561..50739836 [GRCh38] Chr22:44298441..51178264 [GRCh37] Chr22:42629774..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:46919818-50739836)x1	copy number loss	See cases [RCV000135615]	Chr22:46919818..50739836 [GRCh38] Chr22:47315714..51178264 [GRCh37] Chr22:45694378..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:50055303-50677724)x3	copy number gain	See cases [RCV000136106]	Chr22:50055303..50677724 [GRCh38] Chr22:50493732..51116152 [GRCh37] Chr22:48835859..49463018 [NCBI36] Chr22:22q13.33	uncertain significance
GRCh38/hg38 22q13.31-13.33(chr22:44797239-50739836)x3	copy number gain	See cases [RCV000136573]	Chr22:44797239..50739836 [GRCh38] Chr22:45193119..51178264 [GRCh37] Chr22:43571783..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:50274967-50739836)x3	copy number gain	See cases [RCV000136874]	Chr22:50274967..50739836 [GRCh38] Chr22:50713396..51178264 [GRCh37] Chr22:49055523..49525130 [NCBI36] Chr22:22q13.33	benign
GRCh38/hg38 22q13.2-13.33(chr22:41871143-50739836)x1	copy number loss	See cases [RCV000136921]	Chr22:41871143..50739836 [GRCh38] Chr22:42267147..51178264 [GRCh37] Chr22:40597093..49525130 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.32-13.33(chr22:48614336-50739836)x1	copy number loss	See cases [RCV000136941]	Chr22:48614336..50739836 [GRCh38] Chr22:49010148..51178264 [GRCh37] Chr22:47396711..49525130 [NCBI36] Chr22:22q13.32-13.33	pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42710276-50739836)x3	copy number gain	See cases [RCV000137136]	Chr22:42710276..50739836 [GRCh38] Chr22:43106282..51178264 [GRCh37] Chr22:41436226..49525130 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:44764289-50739836)x1	copy number loss	See cases [RCV000136894]	Chr22:44764289..50739836 [GRCh38] Chr22:45160169..51178264 [GRCh37] Chr22:43538833..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.32-13.33(chr22:48500344-50780581)x1	copy number loss	See cases [RCV000137377]	Chr22:48500344..50780581 [GRCh38] Chr22:48896156..51203353 [GRCh37] Chr22:47274820..49565875 [NCBI36] Chr22:22q13.32-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:50149563-50780522)x1	copy number loss	See cases [RCV000140089]	Chr22:50149563..50780522 [GRCh38] Chr22:50587992..51218950 [GRCh37] Chr22:48930119..49565816 [NCBI36] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:49535113-50780581)x1	copy number loss	See cases [RCV000139655]	Chr22:49535113..50780581 [GRCh38] Chr22:49928762..51203353 [GRCh37] Chr22:48314766..49565875 [NCBI36] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42837094-50735806)x1	copy number loss	See cases [RCV000141415]	Chr22:42837094..50735806 [GRCh38] Chr22:43233100..51174234 [GRCh37] Chr22:41563044..49521100 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:43187980-50745444)x1	copy number loss	See cases [RCV000140901]	Chr22:43187980..50745444 [GRCh38] Chr22:43583986..51183872 [GRCh37] Chr22:41913930..49530738 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:46732445-50780522)x1	copy number loss	See cases [RCV000140772]	Chr22:46732445..50780522 [GRCh38] Chr22:47128342..51218950 [GRCh37] Chr22:45507006..49565816 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:50485457-50759410)x1	copy number loss	See cases [RCV000142303]	Chr22:50485457..50759410 [GRCh38] Chr22:50923886..51197838 [GRCh37] Chr22:49270752..49544704 [NCBI36] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42080077-50739836)x3	copy number gain	See cases [RCV000142755]	Chr22:42080077..50739836 [GRCh38] Chr22:42476081..51178264 [GRCh37] Chr22:40806027..49525130 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.32-13.33(chr22:48241375-50739836)x1	copy number loss	See cases [RCV000142589]	Chr22:48241375..50739836 [GRCh38] Chr22:48637187..51178264 [GRCh37] Chr22:47015851..49525130 [NCBI36] Chr22:22q13.32-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:50560890-50739829)x3	copy number gain	See cases [RCV000143203]	Chr22:50560890..50739829 [GRCh38] Chr22:50999319..51178257 [GRCh37] Chr22:49346185..49525123 [NCBI36] Chr22:22q13.33	uncertain significance
GRCh38/hg38 22q13.33(chr22:49529760-50759410)x1	copy number loss	See cases [RCV000143708]	Chr22:49529760..50759410 [GRCh38] Chr22:49923409..51197838 [GRCh37] Chr22:48309413..49544704 [NCBI36] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:46361165-50759299)x1	copy number loss	See cases [RCV000143487]	Chr22:46361165..50759299 [GRCh38] Chr22:46757062..51197727 [GRCh37] Chr22:45135726..49544593 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:50368887-50599372)x3	copy number gain	See cases [RCV000148204]	Chr22:50368887..50599372 [GRCh38] Chr22:50807316..51037801 [GRCh37] Chr22:49154182..49384667 [NCBI36] Chr22:22q13.33	uncertain significance
GRCh38/hg38 22q13.2-13.33(chr22:42138114-50739836)x1	copy number loss	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051370]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051370]\|See cases [RCV000051370]	Chr22:42138114..50739836 [GRCh38] Chr22:42513525..51178264 [GRCh37] Chr22:40843471..49525130 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42433752-50738932)x1	copy number loss	See cases [RCV000051371]	Chr22:42433752..50738932 [GRCh38] Chr22:42829758..51177360 [GRCh37] Chr22:41159702..49524226 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:44740175-50739836)x1	copy number loss	See cases [RCV000051410]	Chr22:44740175..50739836 [GRCh38] Chr22:45136055..51178264 [GRCh37] Chr22:43514719..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:45648256-50739836)x1	copy number loss	See cases [RCV000051411]	Chr22:45648256..50739836 [GRCh38] Chr22:46044136..51178264 [GRCh37] Chr22:44422800..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:47122613-50739836)x1	copy number loss	See cases [RCV000051412]	Chr22:47122613..50739836 [GRCh38] Chr22:47518509..51178264 [GRCh37] Chr22:45897173..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:47234701-50739836)x1	copy number loss	See cases [RCV000051413]	Chr22:47234701..50739836 [GRCh38] Chr22:47630451..51178264 [GRCh37] Chr22:46009115..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:33768441-50739977)x3	copy number gain	See cases [RCV000051682]	Chr22:33768441..50739977 [GRCh38] Chr22:34164428..51178405 [GRCh37] Chr22:32494428..49525271 [NCBI36] Chr22:22q12.3-13.33	pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:37061769-50738932)x3	copy number gain	See cases [RCV000051684]	Chr22:37061769..50738932 [GRCh38] Chr22:37457809..51177360 [GRCh37] Chr22:35787755..49524226 [NCBI36] Chr22:22q12.3-13.33	pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42599757-50725241)x3	copy number gain	See cases [RCV000051686]	Chr22:42599757..50725241 [GRCh38] Chr22:42995763..51163669 [GRCh37] Chr22:41325707..49510535 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:47705262-50739836)x1	copy number loss	See cases [RCV000050848]	Chr22:47705262..50739836 [GRCh38] Chr22:48101011..51178264 [GRCh37] Chr22:46479675..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:46065705-50739836)x1	copy number loss	See cases [RCV000051098]	Chr22:46065705..50739836 [GRCh38] Chr22:46461585..51178264 [GRCh37] Chr22:44840249..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:45239376-50739836)x1	copy number loss	See cases [RCV000050935]	Chr22:45239376..50739836 [GRCh38] Chr22:45635257..51178264 [GRCh37] Chr22:44013921..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:50368887-50599372)x3	copy number gain	See cases [RCV000052894]	Chr22:50368887..50599372 [GRCh38] Chr22:50807316..51037801 [GRCh37] Chr22:49154182..49384667 [NCBI36] Chr22:22q13.33	uncertain significance
NC_000022.11:g.50583199GGCGGCGG[3]	microsatellite	not provided [RCV001666564]	Chr22:50583192..50583193 [GRCh38] Chr22:51021621..51021622 [GRCh37] Chr22:22q13.33	benign
NM_005198.4(CHKB):c.-389G>A	single nucleotide variant	not provided [RCV000826859]	Chr22:50583170 [GRCh38] Chr22:51021599 [GRCh37] Chr22:22q13.33	benign
NM_005198.4(CHKB):c.-369T>G	single nucleotide variant	not provided [RCV000826860]	Chr22:50583150 [GRCh38] Chr22:51021579 [GRCh37] Chr22:22q13.33	benign
NM_005198.4(CHKB):c.-553C>G	single nucleotide variant	not provided [RCV000831030]	Chr22:50583334 [GRCh38] Chr22:51021763 [GRCh37] Chr22:22q13.33	benign
NM_005198.4(CHKB):c.-269C>T	single nucleotide variant	not provided [RCV000837049]	Chr22:50583050 [GRCh38] Chr22:51021479 [GRCh37] Chr22:22q13.33	benign
NC_000022.11:g.43032129_50739836del	deletion	Phelan-McDermid syndrome [RCV001254356]	Chr22:43032129..50739836 [GRCh38] Chr22:22q13.2-13.33	pathogenic
NC_000022.11:g.47513236_50806138del	deletion	Phelan-McDermid syndrome [RCV001254357]	Chr22:47513236..50806138 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.45708330_50737364del	deletion	Phelan-McDermid syndrome [RCV001254359]	Chr22:45708330..50737364 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.48500344_50780581del	deletion	Phelan-McDermid syndrome [RCV001254361]	Chr22:48500344..50780581 [GRCh38] Chr22:22q13.32-13.33	pathogenic
NC_000022.11:g.47447433_50806138del	deletion	Phelan-McDermid syndrome [RCV001254362]	Chr22:47447433..50806138 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.47705262_50739836del	deletion	Phelan-McDermid syndrome [RCV001254360]	Chr22:47705262..50739836 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.47823120_50759410del	deletion	Phelan-McDermid syndrome [RCV001254355]	Chr22:47823120..50759410 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.49181210_50759297del	deletion	Phelan-McDermid syndrome [RCV001254368]	Chr22:49181210..50759297 [GRCh38] Chr22:22q13.33	pathogenic
NC_000022.11:g.44245760_50806121del	deletion	Phelan-McDermid syndrome [RCV001254369]	Chr22:44245760..50806121 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.46269281_50740560del	deletion	Phelan-McDermid syndrome [RCV001254358]	Chr22:46269281..50740560 [GRCh38] Chr22:22q13.31-13.33	pathogenic
Single allele	duplication	not provided [RCV002227667]	Chr22:50023390..50594061 [GRCh38] Chr22:22q13.33	uncertain significance
GRCh38/hg38 22q13.31-13.33(chr22:44549957-50789329)	copy number loss	Phelan-McDermid syndrome [RCV003986080]	Chr22:44549957..50789329 [GRCh38] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.1-13.33(chr22:40202014-50735806)x3	copy number gain	See cases [RCV000134513]	Chr22:40202014..50735806 [GRCh38] Chr22:40598018..51174234 [GRCh37] Chr22:38927964..49521100 [NCBI36] Chr22:22q13.1-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43992879-50683114)x3	copy number gain	See cases [RCV000136124]	Chr22:43992879..50683114 [GRCh38] Chr22:44388759..51121542 [GRCh37] Chr22:42720092..49468408 [NCBI36] Chr22:22q13.31-13.33	benign
GRCh38/hg38 22q13.2-13.33(chr22:42380961-50759410)x3	copy number gain	See cases [RCV000141659]	Chr22:42380961..50759410 [GRCh38] Chr22:42776967..51197838 [GRCh37] Chr22:41106911..49544704 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42826246-50739836)x1	copy number loss	See cases [RCV000051407]	Chr22:42826246..50739836 [GRCh38] Chr22:43222252..51178264 [GRCh37] Chr22:41552196..49525130 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43807366-50739836)x1	copy number loss	See cases [RCV000051408]	Chr22:43807366..50739836 [GRCh38] Chr22:44203246..51178264 [GRCh37] Chr22:42534579..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43993654-50739977)x1	copy number loss	See cases [RCV000051409]	Chr22:43993654..50739977 [GRCh38] Chr22:44389534..51178405 [GRCh37] Chr22:42720867..49525271 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.32-13.33(chr22:48138038-50739836)x1	copy number loss	See cases [RCV000051440]	Chr22:48138038..50739836 [GRCh38] Chr22:48533855..51178264 [GRCh37] Chr22:46912519..49525130 [NCBI36] Chr22:22q13.32-13.33	pathogenic
GRCh38/hg38 22q13.32-13.33(chr22:48423668-50739836)x1	copy number loss	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051441]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051441]\|See cases [RCV000051441]	Chr22:48423668..50739836 [GRCh38] Chr22:48819480..51178264 [GRCh37] Chr22:47198144..49525130 [NCBI36] Chr22:22q13.32-13.33	pathogenic
GRCh38/hg38 22q13.32-13.33(chr22:48654672-50739836)x1	copy number loss	See cases [RCV000051442]	Chr22:48654672..50739836 [GRCh38] Chr22:49050484..51178264 [GRCh37] Chr22:47436920..49525130 [NCBI36] Chr22:22q13.32-13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:49395349-50738932)x1	copy number loss	See cases [RCV000051443]	Chr22:49395349..50738932 [GRCh38] Chr22:49788999..51177360 [GRCh37] Chr22:48175003..49524226 [NCBI36] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42653747-50739836)x3	copy number gain	See cases [RCV000051687]	Chr22:42653747..50739836 [GRCh38] Chr22:43049753..51178264 [GRCh37] Chr22:41379697..49525130 [NCBI36] Chr22:22q13.2-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:44700812-50739836)x3	copy number gain	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051688]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051688]\|See cases [RCV000051688]	Chr22:44700812..50739836 [GRCh38] Chr22:45096692..51178264 [GRCh37] Chr22:43475356..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:44811200-50739836)x3	copy number gain	See cases [RCV000051689]	Chr22:44811200..50739836 [GRCh38] Chr22:45207080..51178264 [GRCh37] Chr22:43585744..49525130 [NCBI36] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.48500337_50739785del	deletion	Phelan-McDermid syndrome [RCV001254365]	Chr22:48500337..50739785 [GRCh38] Chr22:22q13.32-13.33	pathogenic
NC_000022.11:g.46489644_50806138del	deletion	Phelan-McDermid syndrome [RCV001254363]	Chr22:46489644..50806138 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.46467175_50759338del	deletion	Phelan-McDermid syndrome [RCV001254367]	Chr22:46467175..50759338 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.43802117_50806121del	deletion	Phelan-McDermid syndrome [RCV001254364]	Chr22:43802117..50806121 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.44702479_50806138del	deletion	Phelan-McDermid syndrome [RCV001254370]	Chr22:44702479..50806138 [GRCh38] Chr22:22q13.31-13.33	pathogenic
NC_000022.11:g.45819932_50737806del	deletion	Phelan-McDermid syndrome [RCV001254366]	Chr22:45819932..50737806 [GRCh38] Chr22:22q13.31-13.33	pathogenic
Single allele	duplication	Chromosome 22q13 duplication syndrome [RCV002280361]	Chr22:49883237..50740457 [GRCh38] Chr22:22q13.33	pathogenic
GRCh38/hg38 22q13.33(chr22:49757859-50740457)x1	copy number loss	Phelan-McDermid syndrome [RCV003327722]	Chr22:49757859..50740457 [GRCh38] Chr22:22q13.33	pathogenic

Predicted Target Of

	Summary Value
Count of predictions:	149
Count of miRNA genes:	138
Interacting mature miRNAs:	142
Transcripts:	ENST00000380711
Prediction methods:	Microtar, Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
597429598	GWAS1525672_H	protein measurement QTL GWAS1525672 (human)		3e-14	protein measurement		22	50583170	50583171	Human
597513803	GWAS1609877_H	choline/ethanolamine kinase measurement QTL GWAS1609877 (human)		2e-15	choline/ethanolamine kinase measurement		22	50586113	50586114	Human
597531588	GWAS1627662_H	2'-deoxyuridine measurement QTL GWAS1627662 (human)		8e-31	2'-deoxyuridine measurement		22	50584995	50584996	Human
597473223	GWAS1569297_H	Myopia QTL GWAS1569297 (human)		0.000002	Myopia		22	50585879	50585880	Human

STS-T55238

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	22	51,019,552 - 51,019,822	UniSTS	GRCh37
Build 36	22	49,366,418 - 49,366,688	RGD	NCBI36
Celera	22	34,895,585 - 34,895,855	RGD
Cytogenetic Map	22	q13.33	UniSTS
HuRef	22	33,910,551 - 33,910,821	UniSTS
GeneMap99-GB4 RH Map	22	173.05	UniSTS

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

adipose tissue	alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	entire extraembryonic component	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
1200	2421	2672	2223	4944	1724	2336	6	622	1851	464	2240	7078	6328	53	3728	848	1740	1603	174	1


RefSeq Transcripts	NR_021492	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NR_110536	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BE393070	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BI561134	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BJ989458	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068256	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CR456603	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CR980518	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U62317	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENST00000380711

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,583,026 - 50,583,877 (+)	Ensembl

Ensembl Acc Id:

ENST00000609758

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,597,152 - 50,597,599 (+)	Ensembl

Ensembl Acc Id:

ENST00000648558

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,583,156 - 50,587,640 (+)	Ensembl

Ensembl Acc Id:

ENST00000652967

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,584,554 - 50,588,027 (+)	Ensembl

Ensembl Acc Id:

ENST00000654355

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,584,343 - 50,588,029 (+)	Ensembl

Ensembl Acc Id:

ENST00000654727

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,586,873 - 50,595,634 (+)	Ensembl

Ensembl Acc Id:

ENST00000656328

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,583,120 - 50,584,333 (+)	Ensembl

Ensembl Acc Id:

ENST00000662119

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,584,405 - 50,588,035 (+)	Ensembl

Ensembl Acc Id:

ENST00000666183

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,583,179 - 50,584,182 (+)	Ensembl

Ensembl Acc Id:

ENST00000803312

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,586,605 - 50,597,592 (+)	Ensembl

Ensembl Acc Id:

ENST00000803313

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	50,583,124 - 50,588,064 (+)	Ensembl

RefSeq Acc Id:

NR_021492

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	22	50,583,026 - 50,583,931 (+)	NCBI
GRCh37	22	51,021,455 - 51,022,356 (+)	NCBI
HuRef	22	33,912,454 - 33,913,355 (+)	NCBI
CHM1_1	22	50,980,188 - 50,981,093 (+)	NCBI
T2T-CHM13v2.0	22	51,093,554 - 51,094,459 (+)	NCBI

Sequence:

show sequence

ACCAATGGTCTCTCTCTGGGCGGGGCTGCTGTTGGACGGCCTGGGCCAATCCGAGGCGCCGGAGGCCAATCAGTTGGCGGAGCGGCGCGTGCGCGGGCGAGGAACTGCCCGGGCGCGGTAGCGTACGG
GAAGACCGGAGAGGAGCTGCGTCTCTGCCCCGTGGGAGCCGGCGGGGCGGCGGGGCGGCGGCTGCAGCTGCAGCTCCGGCGCGAGGGCTCCCTTGCCGGGCCCTCTTCCCCGACCCCTGGGGCGCTCC
GACAAGGAAGAGCCGTCCAGCGCGCGTCCGTCCTGAGCGTGGGCCTAGAACCAATTACAGAGTCAAACCCAAGAGCCGAAGAAAGTGAAGACTCGCAGCTTGCCGCAGCCCCCTCCTCGGCCTGCGCA
CCTCCCATTGAGGGCGTCCTGATTTAAACGCGTGCCTCCTGCATTTCTGCTTCTGCCCCAGGCTAGAGCGGCGACCAGGAACGCTGGACCCACAGAGATCTGTGGCAATGTCTGTCGAACCATGGTGT
TCTTTGGGGCATCTGACTAGAGTATTGTTTGATAACCAGAAAGAAATCAAAAATTGGTGATCACAAGGCTAATGTCACTTTTGCTGCAGTGGAAAATCATGATCATTCTGTTTAAATCTG

hide sequence

RefSeq Acc Id:

NR_110536

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	22	50,583,026 - 50,595,281 (+)	NCBI
CHM1_1	22	50,980,188 - 50,992,377 (+)	NCBI
T2T-CHM13v2.0	22	51,093,554 - 51,105,799 (+)	NCBI

Sequence:

show sequence

ACCAATGGTCTCTCTCTGGGCGGGGCTGCTGTTGGACGGCCTGGGCCAATCCGAGGCGCCGGAGGCCAATCAGTTGGCGGAGCGGCGCGTGCGCGGGCGAGGAACTGCCCGGGCGCGGTAGCGTACGG
GAAGACCGGAGAGGAGCTGCGTCTCTGCCCCGTGGGAGCCGGCGGGGCGGCGGGGCGGCGGCTGCAGCTGCAGCTCCGGCGCGAGGGCTCCCTTGCCGGGCCCTCTTCCCCGACCCCTGGGGCGCTCC
GACAAGGAAGAGCCGTCCAGCGCGCGTCCGTCCTGAGCGTGGGGTCCCAGGCCAGCATCACTATCCAGGAGCTTCAGGCATGCTCCGTGTACCAACATGGGATCACGAATCACATCGCCTCAGGCCAA
GAAAGCCATTTTATAGCGAAAGAGCCTTAGGATCTGCTGGATTAGAGCCTGTTTCCCAGGTAGGAACGCTTCCACGAGGGCACTCCTGCTGGTTGCAGGAAGGATACCTCTGCTGAGCCTGAATCTGC
AAAGACCACCAGGTTACTCTCAGCTCCTCATACTGGTGGACCAGCAGGCCACAAAGGAGGGGATACTTGATCCTGATAAACGGTTATGCTTGTTTGCTGATGGAAATGATCCAGAAGAGAAGGACAAG
TTGACGATTGAGAGGGTTAATGTCAGGTAAGAAACTTGAGTGGAC

hide sequence


GenBank Protein	CAG30489	(Get FASTA)	NCBI Sequence Viewer

RGD ID:

15097417

Promoter ID:

EPDNEWNC_H2257

Type:

initiation region

Name:

CHKB-DT_1

Description:

CHKB divergent transcript [Source:HGNCSymbol;Acc:HGNC:40146]

SO ACC ID:

SO:0000170

Source:

EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	22	50,583,124 - 50,583,184	EPDNEWNC

Database	Acc Id	Source(s)
COSMIC	CHKB-DT	COSMIC
Ensembl Genes	ENSG00000205559	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000380711	ENTREZGENE
GTEx	ENSG00000205559	GTEx
HGNC ID	HGNC:40146	ENTREZGENE
Human Proteome Map	CHKB-DT	Human Proteome Map
NCBI Gene	CHKB-AS1	ENTREZGENE
RNAcentral	URS00004A51D4	RNACentral
	URS000075C6FC	RNACentral
	URS000075CF9B	RNACentral
	URS0000DBB165	RNACentral
	URS0000EEE308	RNACentral
	URS0000EEED17	RNACentral
	URS0000EF021B	RNACentral
	URS0000EF3061	RNACentral
	URS0000EF316B	RNACentral
	URS0000EF3822	RNACentral

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2018-03-27	CHKB-DT	CHKB divergent transcript	CHKB-AS1	CHKB antisense RNA 1 (head to head)	Symbol and/or name change	5135510	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailable


InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailable


Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
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Imported Disease Annotations - ClinVar