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GeneBe

SFRP2

secreted frizzled related protein 2, the group of Secreted frizzled-related proteins

Basic information

Region (hg38): 4:153780590-153789083

Links

ENSG00000145423NCBI:6423OMIM:604157HGNC:10777Uniprot:Q96HF1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SFRP2 gene.

  • Inborn genetic diseases (7 variants)
  • not provided (3 variants)
  • Anophthalmia-microphthalmia syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFRP2 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
1
clinvar
1
clinvar
2
missense
7
clinvar
1
clinvar
8
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 7 2 1

Variants in SFRP2

This is a list of pathogenic ClinVar variants found in the SFRP2 region.

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

Position Type Phenotype Significance ClinVar
4-153781467-C-T not specified Uncertain significance (Dec 31, 2023)3160903
4-153781540-C-T not specified Uncertain significance (Sep 20, 2023)3160902
4-153781567-G-C not specified Uncertain significance (May 05, 2023)2567547
4-153781664-G-A Likely benign (Jul 27, 2018)753909
4-153781713-T-C Anophthalmia-microphthalmia syndrome Likely benign (Jan 01, 2013)221956
4-153781732-T-A not specified Uncertain significance (May 06, 2022)2287938
4-153781759-T-A Benign (Jun 29, 2018)776024
4-153785903-C-A not specified Uncertain significance (Dec 21, 2022)2377656
4-153785908-T-C not specified Uncertain significance (Mar 23, 2023)2528651
4-153788505-T-G not specified Uncertain significance (Feb 28, 2024)3160901
4-153788590-C-T Benign (Jun 29, 2018)776025
4-153788631-T-C not specified Uncertain significance (Jun 11, 2021)2232552
4-153788745-G-C not specified Uncertain significance (Dec 09, 2023)3160904
4-153788757-G-C not specified Uncertain significance (Nov 08, 2021)2259224
4-153788789-T-C not specified Uncertain significance (Feb 27, 2023)2489240

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SFRP2protein_codingprotein_codingENST00000274063 38529
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001670.9001257240241257480.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.311191670.7140.000008961947
Missense in Polyphen5376.9980.68833881
Synonymous-1.709071.71.250.00000422558
Loss of Function1.44611.20.5365.72e-7123

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002800.000275
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.0001390.000139
European (Non-Finnish)0.00007050.0000703
Middle Eastern0.0001630.000163
South Asian0.0001310.000131
Other0.0001630.000163

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. SFRP2 may be important for eye retinal development and for myogenesis.;
Pathway
Wnt signaling pathway - Homo sapiens (human);WNT-Ncore;Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;Negative regulation of TCF-dependent signaling by WNT ligand antagonists;Wnt Canonical;TCF dependent signaling in response to WNT;Wnt Mammals (Consensus)

Recessive Scores

pRec
0.350

Intolerance Scores

loftool
0.454
rvis_EVS
-0.14
rvis_percentile_EVS
43.29

Haploinsufficiency Scores

pHI
0.889
hipred
Y
hipred_score
0.721
ghis
0.507

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.994

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sfrp2
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; embryo 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); growth/size/body region phenotype; reproductive system phenotype; normal 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); craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process
branching involved in blood vessel morphogenesis;chondrocyte development;outflow tract morphogenesis;cardiac left ventricle morphogenesis;apoptotic process;cell-cell signaling;response to nutrient;positive regulation of cell population proliferation;negative regulation of cell population proliferation;male gonad development;regulation of signaling receptor activity;negative regulation of gene expression;negative regulation of cardiac muscle cell apoptotic process;negative regulation of epithelial to mesenchymal transition;positive regulation of endopeptidase activity;regulation of neuron projection development;negative regulation of Wnt signaling pathway;collagen fibril organization;positive regulation of cell growth;negative regulation of cell growth;negative regulation of cell migration;negative regulation of BMP signaling pathway;cellular response to extracellular stimulus;positive regulation of peptidyl-serine phosphorylation;positive regulation of cell adhesion mediated by integrin;non-canonical Wnt signaling pathway;post-anal tail morphogenesis;response to drug;negative regulation of mesodermal cell fate specification;embryonic digit morphogenesis;positive regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of JUN kinase activity;positive regulation of fat cell differentiation;positive regulation of osteoblast differentiation;positive regulation of angiogenesis;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;digestive tract morphogenesis;negative regulation of epithelial cell proliferation;negative regulation of peptidyl-tyrosine phosphorylation;convergent extension involved in axis elongation;canonical Wnt signaling pathway;bone morphogenesis;sclerotome development;negative regulation of dermatome development;hematopoietic stem cell proliferation;cellular response to X-ray;negative regulation of canonical Wnt signaling pathway;planar cell polarity pathway involved in neural tube closure;Wnt signaling pathway involved in somitogenesis;positive regulation of canonical Wnt signaling pathway;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage;regulation of midbrain dopaminergic neuron differentiation;regulation of stem cell division;negative regulation of planar cell polarity pathway involved in axis elongation
Cellular component
extracellular space;collagen-containing extracellular matrix
Molecular function
fibronectin binding;integrin binding;Wnt-protein binding;receptor ligand activity;endopeptidase activator activity