SPRED3
Basic information
Region (hg38): 19:38388421-38399587
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 SPRED3 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 | |||||
missense | 40 | 40 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 40 | 0 | 1 |
Variants in SPRED3
This is a list of pathogenic ClinVar variants found in the SPRED3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
19-38390376-G-T | not specified | Uncertain significance (Feb 19, 2025) | ||
19-38390394-T-A | not specified | Uncertain significance (Dec 16, 2024) | ||
19-38390408-G-A | not specified | Uncertain significance (May 31, 2023) | ||
19-38390424-G-T | not specified | Uncertain significance (Oct 06, 2024) | ||
19-38390426-G-T | not specified | Uncertain significance (Mar 25, 2024) | ||
19-38390427-G-A | not specified | Uncertain significance (Nov 21, 2024) | ||
19-38390427-G-T | not specified | Uncertain significance (Mar 25, 2024) | ||
19-38390433-G-A | not specified | Uncertain significance (Oct 06, 2024) | ||
19-38390433-G-C | not specified | Uncertain significance (Mar 15, 2024) | ||
19-38390455-C-T | Benign (Jun 01, 2018) | |||
19-38390478-A-G | not specified | Uncertain significance (Jul 14, 2024) | ||
19-38392094-C-T | not specified | Uncertain significance (Jun 26, 2024) | ||
19-38394659-A-G | not specified | Uncertain significance (Feb 02, 2024) | ||
19-38394661-T-G | not specified | Uncertain significance (Feb 02, 2024) | ||
19-38394662-C-A | not specified | Uncertain significance (Feb 02, 2024) | ||
19-38394744-C-A | not specified | Uncertain significance (May 15, 2024) | ||
19-38394761-C-A | not specified | Uncertain significance (Apr 08, 2024) | ||
19-38394764-A-G | not specified | Uncertain significance (Dec 14, 2024) | ||
19-38394767-G-T | not specified | Uncertain significance (Mar 28, 2023) | ||
19-38394772-C-T | not specified | Uncertain significance (Feb 27, 2023) | ||
19-38394776-C-T | not specified | Uncertain significance (Jan 20, 2025) | ||
19-38394781-G-A | not specified | Uncertain significance (Aug 17, 2022) | ||
19-38395505-C-T | not specified | Uncertain significance (Dec 02, 2021) | ||
19-38395546-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
19-38395567-G-A | not specified | Uncertain significance (May 29, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SPRED3 | protein_coding | protein_coding | ENST00000338502 | 5 | 7821 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.212 | 0.780 | 124782 | 0 | 6 | 124788 | 0.0000240 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.43 | 122 | 175 | 0.695 | 0.0000113 | 2473 |
Missense in Polyphen | 42 | 81.836 | 0.51322 | 1242 | ||
Synonymous | 0.819 | 71 | 80.3 | 0.884 | 0.00000553 | 918 |
Loss of Function | 2.29 | 3 | 11.3 | 0.266 | 6.15e-7 | 139 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000869 | 0.0000869 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000177 | 0.0000177 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.000165 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Tyrosine kinase substrate that inhibits growth-factor- mediated activation of MAP kinase. {ECO:0000250}.;
- Pathway
- Signal Transduction;Regulation of RAS by GAPs;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades
(Consensus)
Recessive Scores
- pRec
- 0.0814
Haploinsufficiency Scores
- pHI
- 0.183
- hipred
- Y
- hipred_score
- 0.678
- ghis
- 0.424
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.626
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Spred3
- Phenotype
Gene ontology
- Biological process
- multicellular organism development;regulation of signal transduction
- Cellular component
- membrane
- Molecular function