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.

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.

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						0
missense			27		1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	1

Variants in SFRP5

This is a list of pathogenic ClinVar variants found in the SFRP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97767521-G-A		not specified	Uncertain significance (Mar 07, 2024)
10-97767533-C-G		not specified	Uncertain significance (Jun 30, 2023)
10-97767537-A-G		not specified	Uncertain significance (Jul 30, 2024)
10-97767575-A-T		not specified	Uncertain significance (May 07, 2024)
10-97767607-C-A		not specified	Uncertain significance (Oct 12, 2022)
10-97767620-C-T		not specified	Uncertain significance (Feb 21, 2024)
10-97767698-T-C		not specified	Uncertain significance (Oct 03, 2022)
10-97767717-C-T		not specified	Uncertain significance (Nov 11, 2024)
10-97767728-A-G		not specified	Uncertain significance (May 06, 2024)
10-97767758-C-T		not specified	Uncertain significance (Feb 22, 2023)
10-97767759-G-A		not specified	Uncertain significance (May 23, 2024)
10-97767773-G-A		not specified	Uncertain significance (Dec 16, 2023)
10-97767786-T-G		not specified	Uncertain significance (Jul 30, 2024)
10-97767816-G-A			Benign (Jun 29, 2018)
10-97767849-G-A		not specified	Uncertain significance (Jan 06, 2023)
10-97769701-C-T		not specified	Uncertain significance (Jun 26, 2024)
10-97771307-G-A		not specified	Uncertain significance (Jan 23, 2024)
10-97771313-G-C		not specified	Uncertain significance (Apr 27, 2024)
10-97771369-G-T		not specified	Uncertain significance (Oct 13, 2023)
10-97771380-A-T		not specified	Uncertain significance (Sep 12, 2024)
10-97771414-C-G		not specified	Uncertain significance (Oct 04, 2022)
10-97771415-T-C		not specified	Uncertain significance (Feb 02, 2022)
10-97771433-C-G		not specified	Uncertain significance (Oct 26, 2021)
10-97771457-G-C		not specified	Uncertain significance (Apr 28, 2022)
10-97771527-C-T			Likely benign (Oct 01, 2024)

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