SH2D1B
Basic information
Region (hg38): 1:162395268-162412138
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 SH2D1B 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in SH2D1B
This is a list of pathogenic ClinVar variants found in the SH2D1B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-162398969-G-A | not specified | Uncertain significance (Sep 13, 2022) | ||
| 1-162399032-T-C | not specified | Uncertain significance (May 05, 2022) | ||
| 1-162402740-T-C | not specified | Uncertain significance (Feb 13, 2024) | ||
| 1-162411886-A-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 1-162411928-A-G | not specified | Uncertain significance (May 21, 2024) | ||
| 1-162411975-G-C | not specified | Uncertain significance (Feb 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SH2D1B | protein_coding | protein_coding | ENST00000367929 | 4 | 16873 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0130 | 0.871 | 125686 | 1 | 60 | 125747 | 0.000243 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.319 | 63 | 70.5 | 0.893 | 0.00000359 | 856 |
| Missense in Polyphen | 18 | 23.058 | 0.78063 | 275 | ||
| Synonymous | -0.393 | 30 | 27.4 | 1.10 | 0.00000151 | 240 |
| Loss of Function | 1.30 | 4 | 7.95 | 0.503 | 5.20e-7 | 84 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00229 | 0.00230 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000969 | 0.0000879 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.000489 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Cytoplasmic adapter regulating receptors of the signaling lymphocytic activation molecule (SLAM) family such as CD84, SLAMF1, LY9 and CD244 (PubMed:11689425). In SLAM signaling seems to cooperate with SH2D1A/SAP. Plays a role in regulation of effector functions of natural killer (NK) cells by controlling signal transduction through CD244/2B4 without effecting its tyrosine phosphorylation; downstream signaling involves PLCG1 and ERK activation (PubMed:24687958). Activation of SLAMF7-mediated NK cell function does not effect receptor tyrosine phosphorylation but distal signaling (By similarity). In the context of NK cell- mediated cytotoxicity does not enhance conjugate formation with target cells but stimulates polarization of the microtubule- organizing center and cytotoxic granules toward the NK cell synapse (PubMed:24687958). Negatively regulates CD40-induced cytokine production in dendritic cells downstream of SLAM family receptors probably by inducing activation of the PI3K pathway to inhibit p38 MAPK and JNK activation (By similarity). {ECO:0000250|UniProtKB:O35324, ECO:0000269|PubMed:11689425, ECO:0000269|PubMed:24687958, ECO:0000305|PubMed:21219180}.;
- Pathway
- Natural killer cell mediated cytotoxicity - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- loftool
- 0.565
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 74.95
Haploinsufficiency Scores
- pHI
- 0.133
- hipred
- N
- hipred_score
- 0.180
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.455
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sh2d1b2
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- adaptive immune response;leukocyte activation involved in immune response;positive regulation of natural killer cell mediated immunity;innate immune response;positive regulation of innate immune response;regulation of immune response
- Cellular component
- cytosol
- Molecular function
- protein binding;protein binding, bridging