Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

ADD to My Gene Set

Comment on Gene

View All Comments on Gene

Basic Info

Approved Symbol	NPHP4
Symbol Alias	SLSN4, KIAA0673, POC10
Approved Name	nephronophthisis 4
Name Alias	nephroretinin, "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"
Location	1p36
Position	chr1:5862811-5992473, -1
External Links	HGNC: 19104 Entrez Gene: 261734 Ensembl: ENSG00000131697 UCSC: uc001alq.2
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Hattori, E.,2009	SNP: rs806104	After the two-stage analysis, markers in this gene remained nominally significant (allelic P<0.05) with the same allele being consistently over-represented in both the first and the follow-up stages.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 22)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005198	structural molecule activity	molecular function	NAS[12006559]	14
GO:0016020	membrane	cellular component	IC[12006559]	137

GO terms by database search (count: 20)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0035329	hippo signaling	biological process	TAS	4
GO:0097546	ciliary base	cellular component	IEA	6
GO:0005813	centrosome	cellular component	IDA[21399614]	34
GO:0045494	photoreceptor cell maintenance	biological process	IEA	2
GO:0005829	cytosol	cellular component	TAS	223
GO:0035869	ciliary transition zone	cellular component	IEA	2
GO:0005515	protein binding	molecular function	IPI[12244321]	563
GO:0035845	photoreceptor cell outer segment organization	biological process	IEA	1
GO:0007165	signal transduction	biological process	NAS[12244321]	136
GO:0030317	sperm motility	biological process	IEA	4
GO:0005923	tight junction	cellular component	IEA	13
GO:0090090	negative regulation of canonical Wnt signaling pathway	biological process	IEA	9
GO:0097470	ribbon synapse	cellular component	IEA	1
GO:0030036	actin cytoskeleton organization	biological process	NAS[12006559]	9
GO:0060041	retina development in camera-type eye	biological process	IEA	4
GO:0007632	visual behavior	biological process	NAS[12205563]	2
GO:0032391	photoreceptor connecting cilium	cellular component	IEA	3
GO:0006996	organelle organization	biological process	TAS	23
GO:0016337	single organismal cell-cell adhesion	biological process	NAS[12006559]	10
GO:0005911	cell-cell junction	cellular component	IDA[21565611]	16

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 2)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
NPHP4	RPGRIP1	NO	in vitro;in vivo;yeast 2-hybrid	16339905
NPHP4	NPHP1	NO	in vitro;in vivo	12244321

Related other genetic factors

Gene related SNPs (count: 28)

Literature-origin SNPs (count: 1)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs806104	chr1:5982874 - 5982874(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(1/0/0)

LD-proxies (count: 27)

rs_ID	Location	Functional Annotation
rs869107	chr1:5934866 - 5934866(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7549324	chr1:5921984 - 5921984(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs2152922	chr1:5941005 - 5941005(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs11120832	chr1:5938960 - 5938960(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1566724	chr1:5942743 - 5942743(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs12033563	chr1:5942013 - 5942013(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs6660956	chr1:5956046 - 5956046(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs11120871	chr1:5948531 - 5948531(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs12079601	chr1:5882687 - 5882687(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs11121956	chr1:5881375 - 5881375(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant
rs11122125	chr1:5905119 - 5905119(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs2312464	chr1:5900443 - 5900443(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs962662	chr1:5918450 - 5918450(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs11120772	chr1:5913715 - 5913715(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs3747988	chr1:5877353 - 5877353(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant
rs1295101	chr1:5996108 - 5996108(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs3747992	chr1:5877108 - 5877108(1)	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant
rs806108	chr1:5991206 - 5991206(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs806111	chr1:5993570 - 5993570(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs11120934	chr1:5977543 - 5977543(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1295111	chr1:5986372 - 5986372(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs4068399	chr1:5974140 - 5974140(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs4908638	chr1:5975453 - 5975453(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs11588889	chr1:5971884 - 5971884(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs4068401	chr1:5973941 - 5973941(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs875574	chr1:5967107 - 5967107(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs12745395	chr1:5969877 - 5969877(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: 5)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
1p35-p36	chr1:0-34300000	1 (1/0/0)
1p33-p36	chr1:0-50200000	1 (0/0/1)
1p36	chr1:0-27600000	1 (0/1/0)
1p36.31	chr1:5300000-7100000	1 (0/0/1)
Chr 1	chr1:0-248956422	2 (0/2/0)

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

Gene relationship with SZ

Gene relationship with MDD

View in gBrowse

Region: chr1:5862811..5992473 View in gBrowse