SHB
SH2 domain containing adaptor protein B, the group of SH2 domain containing
Basic information
Region (hg38): 9:37915898-38069227
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (105 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHB gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003028.3. 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 | 5 | |||||
| missense | 102 | 104 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 102 | 4 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SHB | protein_coding | protein_coding | ENST00000377707 | 6 | 150080 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.969 | 0.0313 | 124814 | 0 | 3 | 124817 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.241 | 246 | 257 | 0.958 | 0.0000148 | 3164 |
| Missense in Polyphen | 57 | 81.636 | 0.69822 | 927 | ||
| Synonymous | 0.447 | 102 | 108 | 0.945 | 0.00000667 | 991 |
| Loss of Function | 3.68 | 2 | 19.6 | 0.102 | 9.21e-7 | 241 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000465 | 0.0000464 |
| European (Non-Finnish) | 0.00000885 | 0.00000883 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Adapter protein which regulates several signal transduction cascades by linking activated receptors to downstream signaling components. May play a role in angiogenesis by regulating FGFR1, VEGFR2 and PDGFR signaling. May also play a role in T-cell antigen receptor/TCR signaling, interleukin-2 signaling, apoptosis and neuronal cells differentiation by mediating basic- FGF and NGF-induced signaling cascades. May also regulate IRS1 and IRS2 signaling in insulin-producing cells. {ECO:0000269|PubMed:10828022, ECO:0000269|PubMed:10837138, ECO:0000269|PubMed:12084069, ECO:0000269|PubMed:12464388, ECO:0000269|PubMed:12520086, ECO:0000269|PubMed:15026417, ECO:0000269|PubMed:15919073, ECO:0000269|PubMed:8806685, ECO:0000269|PubMed:9484780, ECO:0000269|PubMed:9751119}.;
- Pathway
- Angiogenesis overview;VEGFA-VEGFR2 Signaling Pathway;Signal Transduction;VEGFA-VEGFR2 Pathway;TCR;EGFR1;IL2;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;Signaling events mediated by VEGFR1 and VEGFR2;PDGFR-alpha signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.121
Haploinsufficiency Scores
- pHI
- 0.320
- hipred
- Y
- hipred_score
- 0.741
- ghis
- 0.438
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.655
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Shb
- 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); 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); reproductive system 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); embryo phenotype;
Gene ontology
- Biological process
- angiogenesis;apoptotic process;signal transduction;positive regulation of signal transduction;cell differentiation;vascular endothelial growth factor receptor signaling pathway
- Cellular component
- nucleoplasm;cytosol;plasma membrane;cytoplasmic ribonucleoprotein granule
- Molecular function
- phosphotyrosine residue binding;SH3/SH2 adaptor activity;protein binding