Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	USP46
Symbol Alias	FLJ12552
Approved Name	ubiquitin specific peptidase 46
Previous Name	ubiquitin specific protease 46
Location	4q12
Position	chr4:52590972-52659335, -1
External Links	HGNC: 20075 Entrez Gene: 64854 Ensembl: ENSG00000109189 UCSC: uc003gzn.3
No. of Studies	1 (Positive: 0; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Kushima, I.,2010	SNP: rs10034164, rs10517263, rs12646800, rs17675844, rs2244291, rs346005, rs6554557	In conclusion, our data argue against the presence of any strong genetic susceptibility factors for bipolar disorder or schizophrenia in the region USP46.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 9)

GO terms by PBA (count: 0)

GO terms by database search (count: 9)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0006511	ubiquitin-dependent protein catabolic process	biological process	IEA	5
GO:0016579	protein deubiquitination	biological process	IDA[14715245]	2
GO:0005515	protein binding	molecular function	IPI[19075014]	563
GO:0032228	regulation of synaptic transmission, GABAergic	biological process	ISS	5
GO:0060013	righting reflex	biological process	IEA	3
GO:0008343	adult feeding behavior	biological process	IEA	2
GO:0001662	behavioral fear response	biological process	IEA	16
GO:0004843	ubiquitin-specific protease activity	molecular function	IDA[14715245]	4
GO:0048149	behavioral response to ethanol	biological process	IEA	6

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 0)

Related other genetic factors

Gene related SNPs (count: 33)

Literature-origin SNPs (count: 7)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs12646800	chr4:52602534 - 52602534(1)	intron_variant; NMD_transcript_variant	1(0/1/0)
rs6554557	chr4:52621374 - 52621374(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant	1(0/1/0)
rs17675844	chr4:52624583 - 52624583(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant	1(0/1/0)
rs2244291	chr4:52602313 - 52602313(1)	intron_variant; NMD_transcript_variant	1(0/1/0)
rs10034164	chr4:52593565 - 52593565(1)	3_prime_UTR_variant; downstream_gene_variant	1(0/1/0)
rs10517263	chr4:52632502 - 52632502(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs346005	chr4:52588572 - 52588572(1)	downstream_gene_variant	1(0/1/0)

LD-proxies (count: 26)

rs_ID	Location	Functional Annotation
rs7662693	chr4:52617076 - 52617076(1)	intron_variant; NMD_transcript_variant
rs7671541	chr4:52613247 - 52613247(1)	intron_variant; NMD_transcript_variant
rs10034052	chr4:52640290 - 52640290(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs10017784	chr4:52628649 - 52628649(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs17051648	chr4:52648024 - 52648024(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs4865395	chr4:52642760 - 52642760(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs10014556	chr4:52657558 - 52657558(1)	intron_variant; NMD_transcript_variant; upstream_gene_variant
rs7668895	chr4:52590250 - 52590250(1)	downstream_gene_variant
rs2270827	chr4:52591254 - 52591254(1)	3_prime_UTR_variant; downstream_gene_variant
rs3733506	chr4:52593454 - 52593454(1)	3_prime_UTR_variant; downstream_gene_variant
rs7675404	chr4:52596998 - 52596998(1)	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant
rs17051586	chr4:52597400 - 52597400(1)	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant
rs6832794	chr4:52599114 - 52599114(1)	intron_variant; NMD_transcript_variant
rs7687075	chr4:52603177 - 52603177(1)	intron_variant; NMD_transcript_variant
rs7693087	chr4:52604987 - 52604987(1)	intron_variant; NMD_transcript_variant
rs17051578	chr4:52587283 - 52587283(1)	downstream_gene_variant
rs13435337	chr4:52587831 - 52587831(1)	downstream_gene_variant
rs13434881	chr4:52588082 - 52588082(1)	downstream_gene_variant
rs6828126	chr4:52588422 - 52588422(1)	downstream_gene_variant
rs7677999	chr4:52590209 - 52590209(1)	downstream_gene_variant
rs12513215	chr4:52643137 - 52643137(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs17051640	chr4:52635364 - 52635364(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7680727	chr4:52606005 - 52606005(1)	intron_variant; NMD_transcript_variant
rs17051576	chr4:52587013 - 52587013(1)	downstream_gene_variant
rs11939490	chr4:52657665 - 52657665(1)	intron_variant; NMD_transcript_variant; upstream_gene_variant
rs7691678	chr4:52647602 - 52647602(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
4q12	chr4:51800000-58500000	1 (0/1/0)
Chr 4	chr4:0-190214555	3 (0/3/0)
4q12-q21	chr4:51800000-87100000	1 (0/0/1)
4q12-q13	chr4:51800000-75300000	1 (0/1/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Description	Result Category
20111060	In conclusion, our data argue against the presence of any strong genetic susceptibility factors for bipolar disorder or schizophrenia in the region USP46.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 1)

Reference	ID in SZGene	Result Category
20111060	932	Negative

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 0)

Overlap with MDD from candidate gene intersection analysis (count: 1)

Reference	Description	Category in MDD	Link in MK4MDD
21663972	We detected an association between the USP46 gene and MDD in a haplotype analysis (rs2244291-rs10034164-rs346005 and rs12646800-rs2244291-rs10034164-rs346005)	Pos	USP46

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Region: chr4:52590972..52659335 View in gBrowse