SH2D2A

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

Basic information

Region (hg38): 1:156806242-156816848

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.

• Inborn genetic diseases (15 variants)
• not provided (8 variants)
• Hereditary insensitivity to pain with anhidrosis (3 variants)
• X-linked lymphoproliferative disease due to SH2D1A deficiency (1 variants)
• not specified (1 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.

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				2		2
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	6	7
Total	0	0	14	4	6

Variants in SH2D2A

This is a list of pathogenic ClinVar variants found in the SH2D2A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-156807267-C-G		not specified	Likely benign (Mar 02, 2023)
1-156809222-C-T		not specified	Uncertain significance (Dec 06, 2023)
1-156809237-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-156809289-C-G		not specified	Uncertain significance (Nov 29, 2023)
1-156809289-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-156809396-G-T		not specified	Uncertain significance (Nov 08, 2022)
1-156809429-A-T		not specified	Uncertain significance (Apr 06, 2023)
1-156809442-G-C		not specified	Uncertain significance (Jul 14, 2023)
1-156809448-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-156809663-C-G		not specified	Uncertain significance (Mar 29, 2022)
1-156809672-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-156813865-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-156813891-A-G		not specified	Uncertain significance (Jul 07, 2022)
1-156813931-G-A		not specified	Uncertain significance (Aug 08, 2023)
1-156813933-G-T		not specified	Likely benign (Jan 16, 2024)
1-156813961-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-156814261-C-G		not specified	Uncertain significance (Oct 28, 2023)
1-156814269-T-C		not specified	Uncertain significance (Dec 07, 2021)
1-156815073-G-T		not specified	Uncertain significance (Oct 12, 2021)
1-156815121-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-156815131-C-T		not specified	Uncertain significance (Apr 19, 2023)
1-156815172-C-T		not specified	Likely benign (Jan 16, 2024)
1-156815564-T-C			Benign (Jun 14, 2018)
1-156815752-AC-A			Benign (Mar 26, 2020)
1-156815821-A-G		NTRK1-related disorder	Likely benign (May 19, 2020)

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