SH2D2A

SH2 domain containing 2A, the group of SH2 domain containing

Basic information

Region (hg38): 1:156806240-156816848

Links

ENSG00000027869

∙ NCBI:9047 ∙ OMIM:604514 ∙ HGNC:10821 ∙ Uniprot:Q9NP31 ∙ 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 SH2D2A gene.

not_specified (49 variants)
not_provided (5 variants)
NTRK1-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH2D2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003975.4. 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			1 clinvar	2 clinvar		3
missense			48 clinvar	3 clinvar		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	55	5	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH2D2A	protein_coding	protein_coding	ENST00000392306	8	10620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.27e-7	0.755	125695	0	50	125745	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.483	200	220	0.908	0.0000117	2532
Missense in Polyphen		50	69.742	0.71693		904
Synonymous	1.04	77	89.6	0.860	0.00000480	825
Loss of Function	1.27	12	17.8	0.675	8.61e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000737	0.000713
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000163	0.000163
South Asian	0.000468	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Could be a T-cell-specific adapter protein involved in the control of T-cell activation. May play a role in the CD4-p56- LCK-dependent signal transduction pathway. Could also play an important role in normal and pathological angiogenesis. Could be an adapter protein that facilitates and regulates interaction of KDR with effector proteins important to endothelial cell survival and proliferation.;
Pathway: VEGF signaling pathway - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;EGF-EGFR Signaling Pathway;Signal Transduction;VEGFA-VEGFR2 Pathway;TCR;ErbB1 downstream signaling;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;VEGF;Signaling events mediated by VEGFR1 and VEGFR2 (Consensus)

Recessive Scores

pRec: 0.118

Intolerance Scores

loftool: 0.562
rvis_EVS: 0.53
rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

pHI: 0.219
hipred: N
hipred_score: 0.461
ghis: 0.400

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.350

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Sh2d2a
Phenotype: immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: angiogenesis;signal transduction;cell population proliferation;positive regulation of signal transduction;cell differentiation;vascular endothelial growth factor receptor signaling pathway
Cellular component: cytoplasm;cytosol
Molecular function: SH3/SH2 adaptor activity;protein binding;SH3 domain binding