SFRP1

secreted frizzled related protein 1, the group of MicroRNA protein coding host genes|Secreted frizzled-related proteins

Basic information

Region (hg38): 8:41261961-41309473

Links

ENSG00000104332 ∙ NCBI:6422 ∙ OMIM:604156 ∙ HGNC:10776 ∙ Uniprot:Q8N474 ∙ 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 SFRP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFRP1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	2

Variants in SFRP1

This is a list of pathogenic ClinVar variants found in the SFRP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-41265178-C-T		not specified	Uncertain significance (Apr 25, 2022)
8-41265299-C-T			Uncertain significance (Feb 28, 2017)
8-41265352-C-T		not specified	Uncertain significance (Sep 29, 2022)
8-41265415-G-C		not specified	Uncertain significance (May 17, 2023)
8-41265420-T-G		not specified	Uncertain significance (Dec 06, 2022)
8-41303480-A-T		not specified	Uncertain significance (Jan 31, 2024)
8-41303532-G-A		not specified	Uncertain significance (Apr 07, 2022)
8-41308640-C-T		not specified	Uncertain significance (Aug 08, 2023)
8-41308658-C-A		not specified	Uncertain significance (Nov 30, 2022)
8-41308659-G-C		not specified	Uncertain significance (Jan 31, 2024)
8-41308711-T-C		not specified	Uncertain significance (Aug 28, 2023)
8-41308916-G-A			Benign (Jun 12, 2018)
8-41308972-G-A		not specified	Likely benign (Apr 07, 2023)
8-41309004-G-A			Benign (Jul 06, 2018)
8-41309011-C-G		not specified	Uncertain significance (Aug 09, 2021)
8-41309024-A-G		not specified	Uncertain significance (Jan 30, 2024)
8-41309026-G-C		not specified	Uncertain significance (Jul 20, 2022)
8-41309155-C-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFRP1	protein_coding	protein_coding	ENST00000220772	3	47536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.965	0.0354	125738	0	2	125740	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	127	176	0.722	0.00000824	2065
Missense in Polyphen		34	67.779	0.50163		789
Synonymous	-0.934	87	76.6	1.14	0.00000397	583
Loss of Function	2.99	0	10.4	0.00	4.40e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000653
Other	0.00	0.00

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. SFRP1 decreases intracellular beta-catenin levels (By similarity). Has antiproliferative effects on vascular cells, in vitro and in vivo, and can induce, in vivo, an angiogenic response. In vascular cell cycle, delays the G1 phase and entry into the S phase (By similarity). In kidney development, inhibits tubule formation and bud growth in metanephroi (By similarity). Inhibits WNT1/WNT4-mediated TCF-dependent transcription. {ECO:0000250}.
• Pathway: Wnt signaling pathway - Homo sapiens (human);WNT-Ncore;Endoderm Differentiation;Vitamin D Receptor Pathway;BMP2-WNT4-FOXO1 Pathway in Human Primary Endometrial Stromal Cell Differentiation;BMP Signaling Pathway in Eyelid Development;Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;Negative regulation of TCF-dependent signaling by WNT ligand antagonists;Wnt;Validated targets of C-MYC transcriptional repression;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.422

Intolerance Scores

• loftool: 0.0932
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.872
• hipred: Y
• hipred_score: 0.759
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfrp1
• Phenotype: limbs/digits/tail 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); skeleton phenotype; immune system phenotype; embryo phenotype; growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); reproductive system phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: osteoblast differentiation;ureteric bud development;positive regulation of cell-matrix adhesion;hematopoietic progenitor cell differentiation;proteolysis;positive regulation of cell population proliferation;negative regulation of cell population proliferation;male gonad development;female gonad development;cellular response to starvation;dorsal/ventral axis specification;regulation of cell cycle process;negative regulation of gene expression;negative regulation of epithelial to mesenchymal transition;regulation of neuron projection development;neural crest cell fate commitment;response to organic cyclic compound;positive regulation of Wnt signaling pathway;negative regulation of Wnt signaling pathway;negative regulation of ossification;positive regulation of cell growth;negative regulation of cell growth;negative regulation of cell migration;negative regulation of BMP signaling pathway;negative regulation of osteoblast proliferation;somatic stem cell population maintenance;non-canonical Wnt signaling pathway;response to drug;positive regulation of apoptotic process;negative regulation of apoptotic process;negative regulation of JUN kinase activity;positive regulation of GTPase activity;cellular response to fibroblast growth factor stimulus;stromal-epithelial cell signaling involved in prostate gland development;negative regulation of B cell differentiation;positive regulation of fat cell differentiation;negative regulation of osteoblast differentiation;negative regulation of osteoclast differentiation;regulation of angiogenesis;positive regulation of smoothened signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;negative regulation of insulin secretion;negative regulation of bone remodeling;negative regulation of fibroblast proliferation;digestive tract morphogenesis;positive regulation of epithelial cell proliferation;negative regulation of epithelial cell proliferation;negative regulation of peptidyl-tyrosine phosphorylation;positive regulation of stress fiber assembly;positive regulation of focal adhesion assembly;canonical Wnt signaling pathway;hematopoietic stem cell differentiation;bone trabecula formation;prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis;regulation of branching involved in prostate gland morphogenesis;negative regulation of androgen receptor signaling pathway;cellular response to vitamin D;cellular response to interleukin-1;cellular response to tumor necrosis factor;cellular response to growth factor stimulus;cellular response to prostaglandin E stimulus;cellular response to estrogen stimulus;cellular response to estradiol stimulus;cellular response to hypoxia;cellular response to X-ray;cellular response to heparin;dopaminergic neuron differentiation;cellular response to transforming growth factor beta stimulus;cellular response to BMP stimulus;negative regulation of canonical Wnt signaling pathway;planar cell polarity pathway involved in neural tube closure;Wnt signaling pathway involved in somitogenesis;convergent extension involved in somitogenesis;positive regulation of canonical Wnt signaling pathway;positive regulation of extrinsic apoptotic signaling pathway via death domain receptors;regulation of midbrain dopaminergic neuron differentiation;negative regulation of planar cell polarity pathway involved in axis elongation;positive regulation of non-canonical Wnt signaling pathway;negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification;negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation;negative regulation of fibroblast apoptotic process;positive regulation of fibroblast apoptotic process
• Cellular component: extracellular region;extracellular space;cytosol;plasma membrane;cell surface;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: cysteine-type endopeptidase activity;frizzled binding;protein binding;drug binding;heparin binding;Wnt-protein binding;identical protein binding