C9orf40 (chromosome 9 open reading frame 40)

Gene: C9orf40 (chromosome 9 open reading frame 40) Homo sapiens

Analyze

Symbol:

C9orf40

Name:

chromosome 9 open reading frame 40

RGD ID:

1350600

HGNC Page

HGNC:23433

Description:

INTERACTS WITH all-trans-retinoic acid; aristolochic acid A; benzo[a]pyrene diol epoxide I

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

FLJ10110; FLJ25795; hypothetical protein LOC55071; uncharacterized protein C9orf40

RGD Orthologs

Alliance Genes

More Info

more info ...

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	9	74,946,583 - 74,952,912 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	74,946,583 - 74,952,912 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	77,561,499 - 77,567,828 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	76,751,319 - 76,757,622 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	74,791,431 - 74,797,356	NCBI
Celera	9	48,135,332 - 48,141,635 (-)	NCBI		Celera
Cytogenetic Map	9	q21.13	NCBI
HuRef	9	47,383,471 - 47,389,771 (-)	NCBI		HuRef
CHM1_1	9	77,707,780 - 77,714,083 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	9	87,099,484 - 87,105,814 (-)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

all-trans-retinoic acid (EXP)

aristolochic acid A (EXP)

benzo[a]pyrene diol epoxide I (EXP)

bisphenol A (ISO)

calcitriol (EXP)

cisplatin (EXP)

copper(II) sulfate (EXP)

coumarin (EXP)

coumestrol (EXP)

cyclosporin A (EXP)

disodium selenite (EXP)

dorsomorphin (EXP)

Enterolactone (EXP)

FR900359 (EXP)

glycidyl methacrylate (EXP)

leflunomide (EXP)

methyl methanesulfonate (EXP)

methylmercury chloride (EXP)

phenylmercury acetate (EXP)

resveratrol (EXP)

SB 431542 (EXP)

sodium arsenite (EXP)

temozolomide (EXP)

testosterone (EXP)

trichostatin A (EXP)

valproic acid (EXP)

References

References - curated

#	Reference Title	Reference Citation
1.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:8125298	PMID:12477932	PMID:14702039	PMID:15164053	PMID:15489334	PMID:17081983	PMID:22658674	PMID:26186194	PMID:26673895	PMID:28514442	PMID:33961781	PMID:37689310

Genomics

Comparative Map Data

C9orf40
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	74,946,583 - 74,952,912 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	74,946,583 - 74,952,912 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	77,561,499 - 77,567,828 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	76,751,319 - 76,757,622 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	74,791,431 - 74,797,356	NCBI
Celera	9	48,135,332 - 48,141,635 (-)	NCBI		Celera
Cytogenetic Map	9	q21.13	NCBI
HuRef	9	47,383,471 - 47,389,771 (-)	NCBI		HuRef
CHM1_1	9	77,707,780 - 77,714,083 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	9	87,099,484 - 87,105,814 (-)	NCBI		T2T-CHM13v2.0

D030056L22Rik
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	18,690,599 - 18,695,793 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	19	18,690,557 - 18,695,792 (+)	Ensembl		GRCm39 Ensembl
GRCm38	19	18,713,235 - 18,718,429 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	18,713,193 - 18,718,428 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	18,787,726 - 18,792,918 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	19	18,780,255 - 18,785,447 (+)	NCBI		MGSCv36	mm8
Celera	19	19,402,013 - 19,407,185 (+)	NCBI		Celera
Cytogenetic Map	19	B	NCBI
cM Map	19	13.2	NCBI

C1h9orf40
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	225,555,300 - 225,559,509 (+)	NCBI		GRCr8
mRatBN7.2	1	216,128,687 - 216,132,896 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	216,128,651 - 216,133,045 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	224,462,248 - 224,466,459 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	231,398,791 - 231,403,001 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	224,216,782 - 224,220,993 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	234,665,904 - 234,670,113 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	234,665,905 - 234,670,113 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	241,765,682 - 241,769,891 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	222,309,341 - 222,313,550 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	1	213,427,725 - 213,431,934 (+)	NCBI		Celera
Cytogenetic Map	1	q51	NCBI

C11H9orf40
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	11	74,111,413 - 74,120,858 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	74,117,352 - 74,123,788 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	49,885,756 - 49,892,188 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	73,799,237 - 73,805,612 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

C1H9orf40
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	83,244,326 - 83,250,356 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	83,243,848 - 83,249,675 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	83,708,547 - 83,714,590 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	83,694,505 - 83,700,406 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	83,694,520 - 83,699,313 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	83,446,040 - 83,452,070 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	83,164,516 - 83,170,544 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	83,924,995 - 83,931,035 (+)	NCBI		UU_Cfam_GSD_1.0

CUNH9orf40
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404946	33,800,065 - 33,800,541 (-)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936837	163,152 - 165,956 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

C1H9orf40
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	228,033,996 - 228,045,013 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	228,038,184 - 228,045,225 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	254,937,432 - 254,944,712 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CUNH9orf40
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	12	85,996,509 - 86,002,835 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	85,996,126 - 86,002,356 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	74,439,986 - 74,446,724 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

CUNH9orf40
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624811	2,570,896 - 2,575,426 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624811	2,529,304 - 2,575,746 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in C9orf40
1 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3	copy number gain	See cases [RCV000050348]	Chr9:193412..138179445 [GRCh38] Chr9:204193..141073897 [GRCh37] Chr9:194193..140193718 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9q21.13(chr9:74887986-75718195)x1	copy number loss	See cases [RCV000052884]	Chr9:74887986..75718195 [GRCh38] Chr9:77502902..78333111 [GRCh37] Chr9:76692722..77522931 [NCBI36] Chr9:9q21.13	uncertain significance
GRCh38/hg38 9q21.13-21.2(chr9:72224348-77332127)x1	copy number loss	See cases [RCV000052906]	Chr9:72224348..77332127 [GRCh38] Chr9:74839264..79947043 [GRCh37] Chr9:74029084..79136863 [NCBI36] Chr9:9q21.13-21.2	pathogenic
GRCh38/hg38 9q21.13-21.31(chr9:73706686-80370629)x1	copy number loss	See cases [RCV000052907]	Chr9:73706686..80370629 [GRCh38] Chr9:76321602..82985544 [GRCh37] Chr9:75511422..82175364 [NCBI36] Chr9:9q21.13-21.31	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3	copy number gain	See cases [RCV000053745]	Chr9:193412..138124532 [GRCh38] Chr9:204193..141018984 [GRCh37] Chr9:194193..140138805 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3	copy number gain	See cases [RCV000053746]	Chr9:193412..138114463 [GRCh38] Chr9:214367..141008915 [GRCh37] Chr9:204367..140128736 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3	copy number gain	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]\|See cases [RCV000053748]	Chr9:193412..138179445 [GRCh38] Chr9:266045..141073897 [GRCh37] Chr9:256045..140193718 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445)	copy number gain	See cases [RCV000133791]	Chr9:204193..138179445 [GRCh38] Chr9:204193..141073897 [GRCh37] Chr9:194193..140193718 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9q21.11-21.13(chr9:68454847-76252863)x1	copy number loss	See cases [RCV000133632]	Chr9:68454847..76252863 [GRCh38] Chr9:71130848..78867779 [GRCh37] Chr9:70259583..78057599 [NCBI36] Chr9:9q21.11-21.13	pathogenic
GRCh38/hg38 9q21.11-31.2(chr9:68420430-106579493)x3	copy number gain	See cases [RCV000136788]	Chr9:68420430..106579493 [GRCh38] Chr9:71130848..109341774 [GRCh37] Chr9:70225166..108381595 [NCBI36] Chr9:9q21.11-31.2	pathogenic
GRCh38/hg38 9q21.11-21.32(chr9:68499530-83670227)x1	copy number loss	See cases [RCV000137963]	Chr9:68499530..83670227 [GRCh38] Chr9:71130848..86285142 [GRCh37] Chr9:70304266..85474962 [NCBI36] Chr9:9q21.11-21.32	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3	copy number gain	See cases [RCV000138783]	Chr9:193412..138124524 [GRCh38] Chr9:204090..141018976 [GRCh37] Chr9:194090..140138797 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9q21.12-31.3(chr9:69627642-111454304)x3	copy number gain	See cases [RCV000139789]	Chr9:69627642..111454304 [GRCh38] Chr9:72242558..114216584 [GRCh37] Chr9:71432378..113256405 [NCBI36] Chr9:9q21.12-31.3	pathogenic
GRCh38/hg38 9p24.3-q22.1(chr9:203861-88130444)x4	copy number gain	See cases [RCV000141904]	Chr9:203861..88130444 [GRCh38] Chr9:203861..90745359 [GRCh37] Chr9:193861..89935179 [NCBI36] Chr9:9p24.3-q22.1	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3	copy number gain	See cases [RCV000141876]	Chr9:203861..138125937 [GRCh38] Chr9:203861..141020389 [GRCh37] Chr9:193861..140140210 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9q21.13(chr9:74282586-75968293)x3	copy number gain	See cases [RCV000141917]	Chr9:74282586..75968293 [GRCh38] Chr9:76897502..78583209 [GRCh37] Chr9:76087322..77773029 [NCBI36] Chr9:9q21.13	uncertain significance
GRCh38/hg38 9p24.3-q21.31(chr9:193412-79877816)x3	copy number gain	See cases [RCV000143012]	Chr9:193412..79877816 [GRCh38] Chr9:204104..82492731 [GRCh37] Chr9:194104..81682551 [NCBI36] Chr9:9p24.3-q21.31	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3	copy number gain	See cases [RCV000143476]	Chr9:203862..138125937 [GRCh38] Chr9:203862..141020389 [GRCh37] Chr9:193862..140140210 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3	copy number gain	See cases [RCV000148113]	Chr9:193412..138179445 [GRCh38] Chr9:204193..141073897 [GRCh37] Chr9:194193..140193718 [NCBI36] Chr9:9p24.3-q34.3	pathogenic
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3	copy number gain	See cases [RCV000139207]	Chr9:193412..138159073 [GRCh38] Chr9:68420641..141053525 [GRCh37] Chr9:67910461..140173346 [NCBI36] Chr9:9p11.2-q34.3	pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3	copy number gain	See cases [RCV000138962]	Chr9:193412..138159073 [GRCh38] Chr9:204104..141053525 [GRCh37] Chr9:194104..140173346 [NCBI36] Chr9:9p24.3-q34.3	pathogenic\|conflicting data from submitters
GRCh37/hg19 9p24.3-q34.3(chr9:163131-141122114)x3	copy number gain	See cases [RCV000240081]	Chr9:163131..141122114 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:62525-141006407)	copy number gain	See cases [RCV000449375]	Chr9:62525..141006407 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:203861-141020389)x3	copy number gain	not specified [RCV003986800]	Chr9:203861..141020389 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:203864-141020389)x3	copy number gain	See cases [RCV000448978]	Chr9:203864..141020389 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9q21.11-21.31(chr9:68734571-83557267)x3	copy number gain	See cases [RCV000510725]	Chr9:68734571..83557267 [GRCh37] Chr9:9q21.11-21.31	pathogenic
GRCh37/hg19 9q21.11-34.3(chr9:71069743-140999928)	copy number gain	Global developmental delay [RCV000626548]	Chr9:71069743..140999928 [GRCh37] Chr9:9q21.11-34.3	likely pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:203862-141020389)	copy number gain	See cases [RCV000512392]	Chr9:203862..141020389 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9q21.13-21.31(chr9:74534790-84014155)x1	copy number loss	not provided [RCV000683165]	Chr9:74534790..84014155 [GRCh37] Chr9:9q21.13-21.31	pathogenic
GRCh37/hg19 9q21.13(chr9:77449280-78560923)x1	copy number loss	not provided [RCV000683153]	Chr9:77449280..78560923 [GRCh37] Chr9:9q21.13	uncertain significance
GRCh37/hg19 9q21.11-21.32(chr9:68999534-84656998)x1	copy number loss	not provided [RCV000683169]	Chr9:68999534..84656998 [GRCh37] Chr9:9q21.11-21.32	pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141122247)x3	copy number gain	not provided [RCV000748055]	Chr9:10590..141122247 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141107672)x3	copy number gain	not provided [RCV000748053]	Chr9:10590..141107672 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:46587-141066491)x3	copy number gain	not provided [RCV000748063]	Chr9:46587..141066491 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141114095)x2	copy number gain	not provided [RCV000748054]	Chr9:10590..141114095 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
Single allele	complex	Glioma [RCV000754871]	Chr9:23524426..87359888 [GRCh37] Chr9:9p21.3-q21.33	likely pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:203861-141020388)x3	copy number gain	not provided [RCV000845900]	Chr9:203861..141020388 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9q21.11-21.31(chr9:70974661-81829792)x1	copy number loss	not provided [RCV000846367]	Chr9:70974661..81829792 [GRCh37] Chr9:9q21.11-21.31	pathogenic
GRCh37/hg19 9q21.11-34.3(chr9:71416475-141020389)x3	copy number gain	not provided [RCV000847808]	Chr9:71416475..141020389 [GRCh37] Chr9:9q21.11-34.3	pathogenic
NC_000009.11:g.12246100_101559378inv	inversion	Recurrent spontaneous abortion [RCV000999471]	Chr9:12246100..101559378 [GRCh37] Chr9:9p23-q22.33	likely pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:353349-141020389)	copy number gain	not specified [RCV002053823]	Chr9:353349..141020389 [GRCh37] Chr9:9p24.3-q34.3	pathogenic
GRCh37/hg19 9p24.3-q21.32(chr9:203861-84155399)	copy number gain	not specified [RCV002053820]	Chr9:203861..84155399 [GRCh37] Chr9:9p24.3-q21.32	pathogenic
GRCh37/hg19 9q21.11-33.2(chr9:71349994-122603410)	copy number gain	not specified [RCV002053853]	Chr9:71349994..122603410 [GRCh37] Chr9:9q21.11-33.2	likely pathogenic
GRCh37/hg19 9p22.1-q33.1(chr9:19356861-119513311)	copy number loss	Distal tetrasomy 15q [RCV002280776]	Chr9:19356861..119513311 [GRCh37] Chr9:9p22.1-q33.1	uncertain significance
GRCh37/hg19 9p24.3-q34.11(chr9:203861-131603223)x3	copy number gain	See cases [RCV002292402]	Chr9:203861..131603223 [GRCh37] Chr9:9p24.3-q34.11	pathogenic
GRCh37/hg19 9q21.13(chr9:76897502-78586137)x3	copy number gain	not specified [RCV003986813]	Chr9:76897502..78586137 [GRCh37] Chr9:9q21.13	uncertain significance
GRCh37/hg19 9q21.11-21.31(chr9:68838523-83340723)x1	copy number loss	not provided [RCV000748447]	Chr9:68838523..83340723 [GRCh37] Chr9:9q21.11-21.31	pathogenic
GRCh37/hg19 9q21.11-22.1(chr9:70966262-90761254)x4	copy number gain	See cases [RCV000512280]	Chr9:70966262..90761254 [GRCh37] Chr9:9q21.11-22.1	pathogenic
GRCh37/hg19 9p24.3-q21.33(chr9:203861-88189913)x3	copy number gain	See cases [RCV000512431]	Chr9:203861..88189913 [GRCh37] Chr9:9p24.3-q21.33	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	516
Count of miRNA genes:	405
Interacting mature miRNAs:	442
Transcripts:	ENST00000376854
Prediction methods:	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.

Markers in Region

WI-12436

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	9	77,561,528 - 77,561,655	UniSTS	GRCh37
Build 36	9	76,751,348 - 76,751,475	RGD	NCBI36
Celera	9	48,135,361 - 48,135,488	RGD
Cytogenetic Map	9	q21.13	UniSTS
HuRef	9	47,383,500 - 47,383,627	UniSTS
GeneMap99-GB4 RH Map	9	261.63	UniSTS
Whitehead-RH Map	9	297.4	UniSTS
NCBI RH Map	9	658.3	UniSTS

SHGC-64302

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	9	77,562,077 - 77,562,248	UniSTS	GRCh37
Build 36	9	76,751,897 - 76,752,068	RGD	NCBI36
Celera	9	48,135,910 - 48,136,081	RGD
Cytogenetic Map	9	q21.13	UniSTS
HuRef	9	47,384,049 - 47,384,220	UniSTS
TNG Radiation Hybrid Map	9	25776.0	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system

circulatory system

endocrine system

exocrine system

hemolymphoid system

hepatobiliary system

integumental system

musculoskeletal system

nervous system

renal system

reproductive system

respiratory system

sensory system

visual system

adipose tissue

appendage

entire extraembryonic component

pharyngeal arch

High

Medium

435

750

458

151

633

695

261

282

Low

2003

2924

1638

574

1188

413

3897

2043

3101

338

765

1352

166

922

2744

Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017998	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AK000972	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK225349	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL158825	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC039588	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BM126413	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471089	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068269	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000376854 ⟹ ENSP00000366050

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	9	74,946,583 - 74,952,912 (-)	Ensembl

RefSeq Acc Id:

NM_017998 ⟹ NP_060468

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	9	74,946,583 - 74,952,912 (-)	NCBI
GRCh37	9	77,561,499 - 77,567,802 (-)	RGD
Build 36	9	76,751,319 - 76,757,622 (-)	NCBI Archive
Celera	9	48,135,332 - 48,141,635 (-)	RGD
HuRef	9	47,383,471 - 47,389,771 (-)	RGD
CHM1_1	9	77,707,780 - 77,714,083 (-)	NCBI
T2T-CHM13v2.0	9	87,099,484 - 87,105,814 (-)	NCBI

Sequence:

show sequence

AGAGTGCGCGCGCGCACGTTGTGCGCAGGTTCGAATCTCCGCCGCTTCGCGGTTGCTTCTCAAC
GTCCGGGCCGCATCTCGGCGGCGGCGAGGGCTGAGCGCGGGAGCTGCCTCCGAGCCGGAGCCCC
AGCCCTAGGCCCTGCGCGAGCTGCCCCGCCCTACCCCCTCCAGCGTCCTGTCGCCTCCTCGCCC
GACTTCGGCCTGTCCCTCTCTCACGCGCTCAGTCCTCGCTCTTCGCCCCCCGCAGCTATCGGCA
CTCGGTCTCCCGCGCCTGGCGGGCTCCGCCCGAGCCTCTGGGCCCATGGCCAAGCGGCGTGCGG
CCGAGCCGGTGACGTTCCACGTGCCTTGGAAGCGGCTCCTGCTTTGCGACTTCGCTGAGCAGCC
GCCGCCACCGCCTCTCTGGATCCGGCCGCCCGGGGTCGCGCATGCTGGGCAGCTCCTCGGCGTC
CCAGAGCAGCACCGAAAGCGCAAAATCGACGCAGGGACCATGGCAGAGCCCTCGGCTTCGCCCA
GCAAGCGCCGTGACAGCGGGGACAACAGCGCCCCGAGCGGCCAGGAGCGTGAGGACCACGGTCT
GGAGACAGGCGATCCGCCGCTGCCGCCGCCGCCCGTACTGCCGGGGCCGGGGGAGGAGCTCCCG
GGCGCCCGGCTCCCGGGGGGCGGTGGCGACGACGGGGCGGGGCGCGCAGGACCCCCGCGGGGAG
ACTGGGGGGTCGCATCGCGCCAGCACAATGAAGAATTTTGGCAGTATAATACCTTCCAGTACTG
GAGGAATCCTTTGCCTCCTATTGATCTGGCAGACATTGAAGATTTAAGTGAAGACACCCTGACA
GAAGCAACACTTCAGGGCAGGAATGAAGGGGCTGAGGTTGACATGGAGTCCTGATGTAAGGAGC
CGAAGCAGTGGGATTGGCTGATTTGAGGAGATGTCTCTAAGTGAATTCTCGTATTCTTAAGGGA
AAAGTTATTTTCCATACTTGAAGTTATATTTCCAAACCTGAGAAATGAAGAAAGATTGTTCTGA
CATTAAATACCTACAGTTACTACTGAACCTCTTAATAAGGATTTGTCAAGGATAGAGTACAGTT
GTAGGGGAAGTATTTTATGTATGCATTCTTAGAGCAAAAAGTTTTGTTTAAATTCTAGAATTGA
AGGTACTGATCTTATAAAAAGAAATTCTAGCAGTTTTAGAAATAGGTGGGAAAAACTCAAATAT
TCCTCCTATCTGCACCAAAAAGTTTATTTGTGGTATATAAAATGAATATTGTTTTATAATAACT
TGTTAATAAAGTACTTTCTAATACATTCTATTGACTCTGTTAGTTGAACAAATAGCTGACTTGA
ACATCTATGCAAACTTAAGATGGGCGGGATTGTTGTAAAAGCTATTGTTTTAAAAGAGCTTTCT
AAATGTAAAGTAGTGATAATTTCAATTTGGGTAGCGTGTTTGCAAAGCTTCCAATATTTGATGT
TGGTTAAGCTCTACTATGGGCAACTGAAGATGGATAAAGAAAAATGAAAACTGAATCGGTGCCT
GCTTCCCCCTGTTTTCCCAGGATTAGAGGAAAAAATTTATTGTATAATCAGCTTCTTGGTTTTG
AATTGCTTCGAGGCATGGTTTTATTCCTTATTACTTTAGACCTGTAGTTTTCAACACTGACAGC
ACTTTAAAAATCTTTGCCTGGGCCTCACTCTTGAGAGATTCTCATTTAATAGTTCTGAGGTGGG
TCTTGGATATAACTATTTTTTTAAACACCTGTCCTGTTTCCCTCCATTCCTCTCATGTGCAGAC
AGGGTTGAGAACCAGTAGACTAATGGTCGTTTTTCCTGTTTAAAGGAGATAACTAATTTGAGCT
GAAGCAATGCTTCTTAATTAGCTTTGTTTTTGTTTTGCTCTGTTGGTGGCTTTGTTACAACTGA
ATTATTGTGTTATTACTATTTCATTGTTAAAGAAATAAAGTAAGCAATTTGTGATGTGAGTATC
AGTGATTAAGTTAACTAACTTTTGTACTGCATCCAGAATGTTGGTTTTGCAATTGAGTAACTGG
TTCTTGCTTGCATTTTTTGTTGTTGATGACATTAGATCCAAAATTCAAGACAAATGGTAAATGC
CATTGAGAGGGAAAGAGAAAAACTTGATTTTTTTTGTGTAATGAAGGATTTAAGAATGGGTTGA
CATTAATAAGAATGCTTTAGAACAGAAGACAAACTGTATTGCATTGTGGTCAGACATGGTTCAA
AGTCTTGTACTGCCACTTCCTACCTATGTATCTTTAAGCCAGTTATTTTTCATCTCCAAGCCTC
AAATTTCTCACCTGTAAAATGAGAAATAATAAATAGTATCTACCTCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_060468	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH39588	(Get FASTA)	NCBI Sequence Viewer
	BAA91449	(Get FASTA)	NCBI Sequence Viewer
	EAW62564	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSP00000366050
	ENSP00000366050.5
GenBank Protein	Q8IXQ3	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_060468 ⟸ NM_017998
- UniProtKB:	Q9NWD3 (UniProtKB/Swiss-Prot), Q8IXQ3 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MAKRRAAEPVTFHVPWKRLLLCDFAEQPPPPPLWIRPPGVAHAGQLLGVPEQHRKRKIDAGTMA EPSASPSKRRDSGDNSAPSGQEREDHGLETGDPPLPPPPVLPGPGEELPGARLPGGGGDDGAGR AGPPRGDWGVASRQHNEEFWQYNTFQYWRNPLPPIDLADIEDLSEDTLTEATLQGRNEGAEVDM ES hide sequence

RefSeq Acc Id:

ENSP00000366050 ⟸ ENST00000376854

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q8IXQ3-F1-model_v2	AlphaFold	Q8IXQ3	1-194	view protein structure

Promoters

RGD ID:

7215265

Promoter ID:

EPDNEW_H13379

Type:

initiation region

Name:

C9orf40_1

Description:

chromosome 9 open reading frame 40

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_H13380

Experiment Methods:

Single-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	9	74,952,851 - 74,952,911	EPDNEW

RGD ID:

7215267

Promoter ID:

EPDNEW_H13380

Type:

initiation region

Name:

C9orf40_2

Description:

chromosome 9 open reading frame 40

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_H13379

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	9	74,952,916 - 74,952,976	EPDNEW

RGD ID:

6807330

Promoter ID:

HG_KWN:63694

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

CD4+TCell, CD4+TCell_12Hour, CD4+TCell_2Hour, HeLa_S3, Jurkat, K562, Lymphoblastoid, NB4

Transcripts:

OTTHUMT00000052702, UC004AJP.2

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	9	76,756,591 - 76,757,672 (-)	MPROMDB

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:23433	AgrOrtholog
COSMIC	C9orf40	COSMIC
Ensembl Genes	ENSG00000135045	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000376854	ENTREZGENE
	ENST00000376854.6	UniProtKB/Swiss-Prot
GTEx	ENSG00000135045	GTEx
HGNC ID	HGNC:23433	ENTREZGENE
Human Proteome Map	C9orf40	Human Proteome Map
InterPro	C9orf40-like	UniProtKB/Swiss-Prot
	WRNPLPNID	UniProtKB/Swiss-Prot
KEGG Report	hsa:55071	UniProtKB/Swiss-Prot
NCBI Gene	55071	ENTREZGENE
PANTHER	CHROMOSOME 9 C9ORF40 HOMOLOG	UniProtKB/Swiss-Prot
	PTHR16003	UniProtKB/Swiss-Prot
Pfam	WRNPLPNID	UniProtKB/Swiss-Prot
PharmGKB	PA134870430	PharmGKB
UniProt	CI040_HUMAN	UniProtKB/Swiss-Prot, ENTREZGENE
	Q9NWD3	ENTREZGENE
UniProt Secondary	Q9NWD3	UniProtKB/Swiss-Prot

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

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

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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