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GeneBe

SFRP5

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

Basic information

Region (hg38): 10:97766750-97771999

Links

ENSG00000120057NCBI:6425OMIM:604158HGNC:10779Uniprot:Q5T4F7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (16 variants)
  • not provided (1 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.

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
16
clinvar
1
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 16 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)3160919
10-97767533-C-G not specified Uncertain significance (Jun 30, 2023)2592340
10-97767607-C-A not specified Uncertain significance (Oct 12, 2022)2349373
10-97767620-C-T not specified Uncertain significance (Feb 21, 2024)3160918
10-97767698-T-C not specified Uncertain significance (Oct 03, 2022)2290253
10-97767758-C-T not specified Uncertain significance (Feb 22, 2023)3160917
10-97767773-G-A not specified Uncertain significance (Dec 16, 2023)3160916
10-97767786-T-G not specified Uncertain significance (Apr 13, 2022)3160915
10-97767816-G-A Benign (Jun 29, 2018)717162
10-97767849-G-A not specified Uncertain significance (Jan 06, 2023)2474459
10-97771307-G-A not specified Uncertain significance (Jan 23, 2024)3160914
10-97771313-G-C not specified Uncertain significance (Jan 26, 2022)3160913
10-97771369-G-T not specified Uncertain significance (Oct 13, 2023)3160912
10-97771414-C-G not specified Uncertain significance (Oct 04, 2022)2321509
10-97771415-T-C not specified Uncertain significance (Feb 02, 2022)2275057
10-97771433-C-G not specified Uncertain significance (Oct 26, 2021)2257221
10-97771457-G-C not specified Uncertain significance (Apr 28, 2022)2286723
10-97771626-G-A not specified Uncertain significance (Nov 01, 2022)2379398
10-97771674-G-A not specified Uncertain significance (Apr 26, 2023)2541330
10-97771692-A-G not specified Uncertain significance (Oct 18, 2021)2255601
10-97771695-A-G not specified Uncertain significance (Jun 30, 2023)2609337
10-97771733-T-C not specified Uncertain significance (Dec 20, 2023)3160909
10-97771769-A-G not specified Uncertain significance (Mar 20, 2023)2526937
10-97771800-T-G not specified Uncertain significance (Feb 15, 2023)2462187
10-97771809-C-G not specified Uncertain significance (Oct 18, 2021)2370078

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SFRP5protein_codingprotein_codingENST00000266066 35202
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000005180.4381256620771257390.000306
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6321611850.8690.000009812031
Missense in Polyphen4861.4850.78068700
Synonymous1.696483.70.7650.00000457634
Loss of Function0.535910.90.8254.66e-7122

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003240.000246
Ashkenazi Jewish0.000.00
East Asian0.0001670.000163
Finnish0.0001390.000139
European (Non-Finnish)0.0005060.000492
Middle Eastern0.0001670.000163
South Asian0.0002950.000294
Other0.0003490.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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