SFRP5
Basic information
Region (hg38): 10:97766751-97771999
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 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) | ||
10-97767575-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) | ||
10-97767728-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 (Apr 13, 2022) | ||
10-97767816-G-A | Benign (Jun 29, 2018) | |||
10-97767849-G-A | not specified | Uncertain significance (Jan 06, 2023) | ||
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) | ||
10-97771414-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) | |||
10-97771580-A-T | not specified | Uncertain significance (Apr 04, 2024) | ||
10-97771626-G-A | not specified | Uncertain significance (Nov 01, 2022) | ||
10-97771674-G-A | not specified | Uncertain significance (Apr 26, 2023) | ||
10-97771692-A-G | not specified | Uncertain significance (Oct 18, 2021) |
GnomAD
Source:
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:
- 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