SHC4
Basic information
Region (hg38): 15:48823741-48963919
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (101 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHC4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000203349.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 72 | 74 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 72 | 2 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SHC4 | protein_coding | protein_coding | ENST00000332408 | 12 | 139710 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
7.11e-11 | 0.866 | 125661 | 0 | 87 | 125748 | 0.000346 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.123 | 349 | 356 | 0.982 | 0.0000181 | 4114 |
Missense in Polyphen | 113 | 120.7 | 0.93619 | 1432 | ||
Synonymous | -0.0447 | 143 | 142 | 1.00 | 0.00000778 | 1237 |
Loss of Function | 1.81 | 21 | 32.1 | 0.655 | 0.00000178 | 355 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000529 | 0.000529 |
Ashkenazi Jewish | 0.00304 | 0.00298 |
East Asian | 0.000386 | 0.000381 |
Finnish | 0.0000464 | 0.0000462 |
European (Non-Finnish) | 0.000169 | 0.000167 |
Middle Eastern | 0.000386 | 0.000381 |
South Asian | 0.000462 | 0.000457 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Activates both Ras-dependent and Ras-independent migratory pathways in melanomas. Contributes to the early phases of agrin-induced tyrosine phosphorylation of CHRNB1. {ECO:0000269|PubMed:17409413}.;
- Pathway
- Chronic myeloid leukemia - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);Breast cancer - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Alcoholism - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Focal Adhesion;Chemokine signaling pathway;Ras Signaling;BDNF
(Consensus)
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- loftool
- 0.766
- rvis_EVS
- -0.71
- rvis_percentile_EVS
- 14.67
Haploinsufficiency Scores
- pHI
- 0.299
- hipred
- Y
- hipred_score
- 0.690
- ghis
- 0.561
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0629
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Shc4
- Phenotype
Gene ontology
- Biological process
- apoptotic process;positive regulation of cell population proliferation;regulation of gene expression;intracellular signal transduction;stem cell differentiation
- Cellular component
- plasma membrane;cell junction;postsynaptic membrane
- Molecular function
- protein binding;protein domain specific binding;receptor tyrosine kinase binding