SFRP5

secreted frizzled related protein 5, the group of Secreted frizzled-related proteins

Basic information

Region (hg38): 10:97766751-97771999

Links

ENSG00000120057

∙ NCBI:6425 ∙ OMIM:604158 ∙ HGNC:10779 ∙ Uniprot:Q5T4F7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SFRP5 gene.

not_specified (58 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFRP5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003015.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			58 clinvar	1 clinvar	1 clinvar	60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFRP5	protein_coding	protein_coding	ENST00000266066	3	5202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000518	0.438	125662	0	77	125739	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.632	161	185	0.869	0.00000981	2031
Missense in Polyphen		48	61.485	0.78068		700
Synonymous	1.69	64	83.7	0.765	0.00000457	634
Loss of Function	0.535	9	10.9	0.825	4.66e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000324	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000506	0.000492
Middle Eastern	0.000167	0.000163
South Asian	0.000295	0.000294
Other	0.000349	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Soluble frizzled-related proteins (sFRPS) function as modulators of Wnt signaling through direct interaction with Wnts. They have a role in regulating cell growth and differentiation in specific cell types. SFRP5 may be involved in determining the polarity of photoreceptor, and perhaps, other cells in the retina.;
Pathway: Wnt signaling pathway - Homo sapiens (human);Wnt Signaling Pathway (Consensus)

Recessive Scores

pRec: 0.192

Intolerance Scores

loftool: 0.872
rvis_EVS: 0.13
rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

pHI: 0.412
hipred: N
hipred_score: 0.409
ghis: 0.516

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Sfrp5
Phenotype: endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; embryo phenotype;

Zebrafish Information Network

Gene name: sfrp5
Affected structure: hepatoblast
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: apoptotic process;establishment or maintenance of cell polarity;signal transduction;multicellular organism development;visual perception;negative regulation of cell population proliferation;anatomical structure morphogenesis;cell differentiation;negative regulation of Wnt signaling pathway;regulation of BMP signaling pathway;non-canonical Wnt signaling pathway;negative regulation of DNA-binding transcription factor activity;negative regulation of protein kinase B signaling;canonical Wnt signaling pathway;negative regulation of canonical Wnt signaling pathway;negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis
Cellular component: extracellular space
Molecular function: Wnt-protein binding