SH2D1B

SH2 domain containing 1B, the group of SH2 domain containing

Basic information

Region (hg38): 1:162395268-162412138

Links

ENSG00000198574

∙ NCBI:117157 ∙ OMIM:608510 ∙ HGNC:30416 ∙ Uniprot:O14796 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SH2D1B gene.

not_specified (16 variants)

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. These statistics are base on transcript: NM_000053282.5. 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			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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