Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	343637
Gene name	R-spondin 4
Gene symbol	RSPO4
Synonyms (NCBI Gene)	C20orf182CRISTIN4
Chromosome	20
Chromosome location	20p13
Summary	This gene encodes a member of the R-spondin family of proteins that share a common domain organization consisting of a signal peptide, cysteine-rich/furin-like domain, thrombospondin domain and a C-terminal basic region. The encoded protein may be involve

Show/Hide all (9)

SNP ID	Visualize variation	Clinical significance	Consequence
rs74315420	T>C	Pathogenic	Coding sequence variant, missense variant
rs74315421	A>G	Pathogenic	Coding sequence variant, missense variant
rs74315422	C>T	Pathogenic	Coding sequence variant, missense variant
rs74315423	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs387907026	G>A	Pathogenic	Coding sequence variant, stop gained
rs387907027	G>A	Pathogenic	Coding sequence variant, missense variant
rs387907028	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs768138495	->C	Pathogenic	Coding sequence variant, frameshift variant
rs775644973	C>T	Pathogenic	Splice donor variant

Show/Hide all (70)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017214	hsa-miR-335-5p	Microarray	18185580
MIRT1321420	hsa-miR-1205	CLIP-seq
MIRT1321421	hsa-miR-1909	CLIP-seq
MIRT1321422	hsa-miR-3123	CLIP-seq
MIRT1321423	hsa-miR-320a	CLIP-seq
MIRT1321424	hsa-miR-320b	CLIP-seq
MIRT1321425	hsa-miR-320c	CLIP-seq
MIRT1321426	hsa-miR-320d	CLIP-seq
MIRT1321427	hsa-miR-3616-3p	CLIP-seq
MIRT1321428	hsa-miR-3925-5p	CLIP-seq
MIRT1321429	hsa-miR-3976	CLIP-seq
MIRT1321430	hsa-miR-4429	CLIP-seq
MIRT1321431	hsa-miR-4728-5p	CLIP-seq
MIRT1321432	hsa-miR-1207-5p	CLIP-seq
MIRT1321433	hsa-miR-2278	CLIP-seq
MIRT1321434	hsa-miR-2861	CLIP-seq
MIRT1321435	hsa-miR-298	CLIP-seq
MIRT1321436	hsa-miR-3150b-3p	CLIP-seq
MIRT1321437	hsa-miR-3154	CLIP-seq
MIRT1321438	hsa-miR-3179	CLIP-seq
MIRT1321439	hsa-miR-3202	CLIP-seq
MIRT1321440	hsa-miR-371-3p	CLIP-seq
MIRT1321441	hsa-miR-3918	CLIP-seq
MIRT1321442	hsa-miR-3919	CLIP-seq
MIRT1321443	hsa-miR-3978	CLIP-seq
MIRT1321444	hsa-miR-4311	CLIP-seq
MIRT1321445	hsa-miR-4419a	CLIP-seq
MIRT1321446	hsa-miR-4428	CLIP-seq
MIRT1321447	hsa-miR-4468	CLIP-seq
MIRT1321448	hsa-miR-4476	CLIP-seq
MIRT1321449	hsa-miR-4497	CLIP-seq
MIRT1321450	hsa-miR-4510	CLIP-seq
MIRT1321451	hsa-miR-4512	CLIP-seq
MIRT1321452	hsa-miR-4514	CLIP-seq
MIRT1321453	hsa-miR-4692	CLIP-seq
MIRT1321454	hsa-miR-4736	CLIP-seq
MIRT1321455	hsa-miR-4756-3p	CLIP-seq
MIRT1321456	hsa-miR-4763-3p	CLIP-seq
MIRT1321457	hsa-miR-4784	CLIP-seq
MIRT1321458	hsa-miR-4802-5p	CLIP-seq
MIRT1321459	hsa-miR-541	CLIP-seq
MIRT1321460	hsa-miR-654-5p	CLIP-seq
MIRT1321461	hsa-miR-939	CLIP-seq
MIRT2095433	hsa-miR-1224-5p	CLIP-seq
MIRT2095434	hsa-miR-2115	CLIP-seq
MIRT2095435	hsa-miR-320e	CLIP-seq
MIRT2095436	hsa-miR-3977	CLIP-seq
MIRT1321447	hsa-miR-4468	CLIP-seq
MIRT2095437	hsa-miR-4663	CLIP-seq
MIRT2095438	hsa-miR-4751	CLIP-seq
MIRT2095439	hsa-miR-499a-5p	CLIP-seq
MIRT2095440	hsa-miR-516a-3p	CLIP-seq
MIRT1321447	hsa-miR-4468	CLIP-seq
MIRT1321447	hsa-miR-4468	CLIP-seq
MIRT2095437	hsa-miR-4663	CLIP-seq
MIRT2095433	hsa-miR-1224-5p	CLIP-seq
MIRT2095434	hsa-miR-2115	CLIP-seq
MIRT2095435	hsa-miR-320e	CLIP-seq
MIRT2095436	hsa-miR-3977	CLIP-seq
MIRT2095438	hsa-miR-4751	CLIP-seq
MIRT2095439	hsa-miR-499a-5p	CLIP-seq
MIRT2095440	hsa-miR-516a-3p	CLIP-seq
MIRT1321436	hsa-miR-3150b-3p	CLIP-seq
MIRT2458661	hsa-miR-3689d	CLIP-seq
MIRT2458662	hsa-miR-4434	CLIP-seq
MIRT2458663	hsa-miR-4459	CLIP-seq
MIRT2458664	hsa-miR-4516	CLIP-seq
MIRT2458665	hsa-miR-4722-5p	CLIP-seq
MIRT1321457	hsa-miR-4784	CLIP-seq
MIRT2458666	hsa-miR-765	CLIP-seq

Show/Hide all (14)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005102	Function	Signaling receptor binding	IBA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	NAS	24431302
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA
GO:0008201	Function	Heparin binding	IEA
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0030177	Process	Positive regulation of Wnt signaling pathway	IDA	29769720
GO:0030177	Process	Positive regulation of Wnt signaling pathway	IEA
GO:0030177	Process	Positive regulation of Wnt signaling pathway	NAS	24431302
GO:0035878	Process	Nail development	IMP	17805348
GO:0060173	Process	Limb development	IEA
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IBA

MIM	HGNC	e!Ensembl
610573	16175	ENSG00000101282

Q2I0M5

Protein name

R-spondin-4 (Roof plate-specific spondin-4) (hRspo4)

Protein function

Activator of the canonical Wnt signaling pathway by acting as a ligand for LGR4-6 receptors (PubMed:29769720). Upon binding to LGR4-6 (LGR4, LGR5 or LGR6), LGR4-6 associate with phosphorylated LRP6 and frizzled receptors that are activated by ex

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF15913	Furin-like_2	35 → 135	Furin-like repeat, cysteine-rich	Domain

Sequence

MRAPLCLLLLVAHAVDMLALNRRKKQVGTGLGGNCTGCIICSEENGCSTCQQRLFLFIRR
EGIRQYGKCLHDCPPGYFGIRGQEVNRCKKCGATCESCFSQDFCIRCKRQFYLYKGKCLP
TCPPGTLAHQNTRECQGECELGPWGGWSPCTHNGKTCGSAWGLESRVREAGRAGHEEAAT
CQVLSESRKCPIQRPCPGERSPGQKKGRKDRRPRKDRKLDRRLDVRPRQPGLQP

Sequence length

234

Interactions

View interactions

	KEGG		Reactome
	Wnt signaling pathway		Regulation of FZD by ubiquitination

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Nonsyndromic congenital nail disorder 4	Pathogenic	rs74315420, rs74315421, rs74315422, rs74315423, rs387907026, rs387907027, rs387907028, rs775644973	RCV000001249 RCV000001250 RCV000001251 RCV000001252 RCV000023830 RCV000023831 RCV000023832 RCV003444150 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ANONYCHIA	—	ClinVar, Disgenet ClinVar, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANONYCHIA CONGENITA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANONYCHIA CONGENITA TOTALIS	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPHERAL NEUROPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RSPO4-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TREATMENT-RESISTANT HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (18)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alzheimer`s Disease	Alzheimer disease	GWASCAT_DG	29274321		★★★★★ ★☆☆☆☆ Found in Text Mining only
ANONYCHIA	Anonychia	BEFREE	17041604, 17186469, 17805348, 17914448, 22300369, 28247548		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANONYCHIA	Anonychia	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANONYCHIA	Anonychia	GENOMICS_ENGLAND_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANONYCHIA	Anonychia	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Anonychia congenita	Anonychia	Pubtator	17186469, 17805348, 17914448, 23234511, 34099859, 36421794	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Anonychia congenita totalis	Anonychia Congenita Totalis	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	BEFREE	28472820		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ectodermal Dysplasia	Ectodermal dysplasia	Pubtator	36421794	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophageal neoplasm	Pubtator	19472401	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	28472820		★★★★★ ★☆☆☆☆ Found in Text Mining only
NAIL DISORDER, NONSYNDROMIC CONGENITAL, 4	Nail Diseases	UNIPROT_DG	17041604		★★★★★ ★☆☆☆☆ Found in Text Mining only
NAIL DISORDER, NONSYNDROMIC CONGENITAL, 4	Nail Diseases	ORPHANET_DG	17914448		★★★★★ ★☆☆☆☆ Found in Text Mining only
NAIL DISORDER, NONSYNDROMIC CONGENITAL, 4	Nail Diseases	GENOMICS_ENGLAND_DG	17914448		★★★★★ ★☆☆☆☆ Found in Text Mining only
NAIL DISORDER, NONSYNDROMIC CONGENITAL, 4	Nail Diseases	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	36611933	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Toenail Dystrophy Isolated	Nail dystrophy	Pubtator	23234511	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
XX males	XX Males	BEFREE	17426450		★★★★★ ★☆☆☆☆ Found in Text Mining only

RSPO4 (R-spondin 4)