Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	4068
Gene name	SH2 domain containing 1A
Gene symbol	SH2D1A
Synonyms (NCBI Gene)	DSHPEBVSIMD5LYPMTCP1SAPSAP/SH2D1AXLPXLPDXLPD1
Chromosome	X
Chromosome location	Xq25
Summary	This gene encodes a protein that plays a major role in the bidirectional stimulation of T and B cells. This protein contains an SH2 domain and a short tail. It associates with the signaling lymphocyte-activation molecule, thereby acting as an inhibitor of

Show/Hide all (16)

SNP ID	Visualize variation	Clinical significance	Consequence
rs111033623	C>T	Pathogenic	Coding sequence variant, stop gained
rs111033624	G>C	Pathogenic	Coding sequence variant, missense variant
rs111033625	T>A,C	Pathogenic, likely-pathogenic	Terminator codon variant, stop lost
rs111033626	C>T	Pathogenic	Coding sequence variant, missense variant
rs111033627	C>T	Pathogenic	Coding sequence variant, missense variant
rs111033628	C>T	Pathogenic	Coding sequence variant, stop gained
rs111033629	G>T	Pathogenic	Initiator codon variant, missense variant
rs111033630	G>T	Pathogenic	Coding sequence variant, missense variant
rs587777612	G>C	Pathogenic	Intron variant
rs1556619319	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1556620697	C>G	Likely-pathogenic	Intron variant
rs1556620698	C>A	Pathogenic	Stop gained, coding sequence variant
rs1556620706	G>A	Pathogenic	Stop gained, coding sequence variant
rs1569527111	A>G	Pathogenic	Coding sequence variant, missense variant
rs1603236465	C>T	Pathogenic	5 prime UTR variant
rs1603238847	G>T	Pathogenic	Splice acceptor variant

Show/Hide all (29)

miRTarBase ID	miRNA	Experiments	Reference
MIRT021557	hsa-miR-142-3p	Microarray	17612493
MIRT722321	hsa-miR-6760-3p	HITS-CLIP	19536157
MIRT722320	hsa-miR-1208	HITS-CLIP	19536157
MIRT722319	hsa-miR-5701	HITS-CLIP	19536157
MIRT722318	hsa-miR-181b-2-3p	HITS-CLIP	19536157
MIRT722317	hsa-miR-181b-3p	HITS-CLIP	19536157
MIRT722316	hsa-miR-4420	HITS-CLIP	19536157
MIRT722315	hsa-miR-653-3p	HITS-CLIP	19536157
MIRT722314	hsa-miR-3606-3p	HITS-CLIP	19536157
MIRT722321	hsa-miR-6760-3p	HITS-CLIP	19536157
MIRT722320	hsa-miR-1208	HITS-CLIP	19536157
MIRT722319	hsa-miR-5701	HITS-CLIP	19536157
MIRT722318	hsa-miR-181b-2-3p	HITS-CLIP	19536157
MIRT722317	hsa-miR-181b-3p	HITS-CLIP	19536157
MIRT722316	hsa-miR-4420	HITS-CLIP	19536157
MIRT722315	hsa-miR-653-3p	HITS-CLIP	19536157
MIRT722314	hsa-miR-3606-3p	HITS-CLIP	19536157
MIRT1344208	hsa-miR-127-5p	CLIP-seq
MIRT1344209	hsa-miR-4795-3p	CLIP-seq
MIRT1344210	hsa-miR-582-5p	CLIP-seq
MIRT1344211	hsa-miR-1206	CLIP-seq
MIRT1344212	hsa-miR-3140-3p	CLIP-seq
MIRT1344213	hsa-miR-3607-5p	CLIP-seq
MIRT1344214	hsa-miR-4777-3p	CLIP-seq
MIRT2326147	hsa-miR-3671	CLIP-seq
MIRT2326148	hsa-miR-520d-5p	CLIP-seq
MIRT2326149	hsa-miR-524-5p	CLIP-seq
MIRT2326150	hsa-miR-556-5p	CLIP-seq
MIRT2326151	hsa-miR-935	CLIP-seq

Show/Hide all (1)

Transcription factor	Regulation	Reference
ATF5	Unknown	18832568

Show/Hide all (19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002250	Process	Adaptive immune response	IEA
GO:0002376	Process	Immune system process	IEA
GO:0005515	Function	Protein binding	IPI	9774102, 10549287, 11389028, 11477068, 11489943, 11806999, 11823424, 12225753, 12545174, 14674764, 15841490, 16920955, 16983070, 20231852, 22912825, 23346089, 24642916, 24688028, 24728074, 25416956, 25910212, 26221972, 32296183, 32814053
GO:0005737	Component	Cytoplasm	IDA	9774102
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	TAS	9774102
GO:0005829	Component	Cytosol	TAS
GO:0006959	Process	Humoral immune response	IEA
GO:0006968	Process	Cellular defense response	IEA
GO:0007267	Process	Cell-cell signaling	IEA
GO:0030101	Process	Natural killer cell activation	IDA	15169881, 15713798, 27249817
GO:0030101	Process	Natural killer cell activation	IDA	15713798
GO:0030674	Function	Protein-macromolecule adaptor activity	IDA	15713798
GO:0042267	Process	Natural killer cell mediated cytotoxicity	IEA
GO:0045087	Process	Innate immune response	IEA
GO:0045954	Process	Positive regulation of natural killer cell mediated cytotoxicity	IEA
GO:0050776	Process	Regulation of immune response	IEA
GO:0050776	Process	Regulation of immune response	IMP	9774102
GO:0050860	Process	Negative regulation of T cell receptor signaling pathway	IDA	9774102

MIM	HGNC	e!Ensembl
300490	10820	ENSG00000183918

O60880

Protein name

SH2 domain-containing protein 1A (Duncan disease SH2-protein) (Signaling lymphocytic activation molecule-associated protein) (SLAM-associated protein) (T-cell signal transduction molecule SAP)

Protein function

Cytoplasmic adapter regulating receptors of the signaling lymphocytic activation molecule (SLAM) family such as SLAMF1, CD244, LY9, CD84, SLAMF6 and SLAMF7. In SLAM signaling seems to cooperate with SH2D1B/EAT-2. Initially it has been proposed t

PDB

1D1Z , 1D4T , 1D4W , 1KA6 , 1KA7 , 1M27

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00017	SH2	6 → 87	SH2 domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed at a high level in thymus and lung, with a lower level of expression in spleen and liver. Expressed in peripheral blood leukocytes, including T-lymphocytes. Tends to be expressed at lower levels in peripheral blood leukocytes

Sequence

MDAVAVYHGKISRETGEKLLLATGLDGSYLLRDSESVPGVYCLCVLYHGYIYTYRVSQTE
TGSWSAETAPGVHKRYFRKIKNLISAFQKPDQGIVIPLQYPVEKKSSARSTQGTTGIRED
PDVCLKAP

Sequence length

128

Interactions

View interactions

	KEGG		Reactome
	Natural killer cell mediated cytotoxicity		Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell

144

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autoinflammatory syndrome	Likely pathogenic; Pathogenic	rs2147531380, rs2147519353, rs2147534056	RCV002264391 RCV002264437 RCV002264508
Thyroid cancer, nonmedullary, 1	Pathogenic	rs1603238847	RCV005887430 RCV005931462
X-linked lymphoproliferative disease due to SH2D1A deficiency	Likely pathogenic; Pathogenic	rs2147519353, rs2147534047, rs746035909, rs2147531379, rs2147531326, rs2147534019, rs2522819003, rs2147534056, rs2522819045, rs2522797198, rs111033623, rs111033628, rs2522814882, rs111033624, rs1603238847 View all (13 more)	RCV001946671 RCV001963121 RCV001949632 RCV002021792 RCV002250349 RCV002250350 RCV002471422 RCV003041479 RCV003041480 RCV003150604 RCV000011645 RCV000011646 RCV000011647 RCV000011648 RCV000011649 RCV000011650 RCV000011651 RCV000011653 RCV000011655 RCV000011657 RCV003510656 RCV003509078 RCV003509079 RCV004560455 RCV000660264 RCV000660265 RCV000660266 RCV000663341 RCV000133459 RCV001246291
X-linked lymphoproliferative syndrome	Pathogenic	rs111033623, rs1569527111	RCV001270156 RCV000781847

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Holoprosencephaly 13, X-linked	Benign; Likely benign	rs72610640	RCV002502408
Lung cancer	Benign; Likely benign	rs72610640	RCV005900605
Lymphoproliferative disorder	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs769919066, rs67202578, rs190741204, rs111033630	RCV001731655 RCV001731656 RCV001731661 RCV004798886
Mullegama-Klein-Martinez syndrome	Benign; Likely benign	rs72610640	RCV002502408
SH2D1A-related disorder	Benign; Uncertain significance; Likely benign	rs370365609, rs2147531344, rs2522814846, rs199706936	RCV003951218 RCV003403759 RCV003969434 RCV003902447
Uterine carcinosarcoma	Benign; Likely benign	rs72610640	RCV005900604

Show/Hide Text Mining Associations (71)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Agammaglobulinemia	Associate	11159547, 11493483, 23944711
AIDS Associated Nephropathy	Associate	12928397
Altitude Sickness	Associate	37841248
Autoimmune Diseases	Associate	24373350, 30990878, 33987447
Autoimmune enteropathy	Associate	32081864
Basal cell carcinoma infundibulocystic	Associate	28943543
Behcet Syndrome	Associate	37264476
Berylliosis	Associate	35972918
Breast Neoplasms	Associate	24495796, 31817155, 34867821
Carcinoma Hepatocellular	Associate	37858067
Combined Saposin Deficiency	Associate	24373350, 31754776
Combined Saposin Deficiency	Inhibit	31754776
Common Variable Immunodeficiency	Associate	11520777, 11678908
Common Variable Immunodeficiency	Inhibit	29083052
Deafness X Linked 1	Associate	40519929
Death	Associate	23944711, 24688028, 29454648
Diabetes Mellitus Type 1	Associate	37576973
Down Syndrome	Associate	21856934
Drug Related Side Effects and Adverse Reactions	Associate	15632210
Dysgammaglobulinemia	Associate	11520777, 19903677
Dyskinesias	Associate	9720876
Encephalitis	Associate	25572984
Epstein Barr Virus Infections	Associate	10852966, 11049992, 11159547, 11493483, 15632210, 16002423, 19425169, 22069374, 23944711, 34987501
Fever	Associate	25572984, 28196537
Genetic Diseases Inborn	Associate	11342640, 1637339
Graves Disease	Associate	33987447
Heredodegenerative Disorders Nervous System	Associate	19997502
HTLV I Infections	Associate	19997502
Hyper IgM Immunodeficiency Syndrome Type 1	Associate	15358621
IgG Deficiency	Associate	19903677
Immune Dysregulation Polyendocrinopathy Enteropathy X Linked Syndrome	Associate	33864888
Immune System Diseases	Associate	11034354, 12766168, 18832568, 37325673, 40226629
Immunologic Deficiency Syndromes	Associate	12766168, 22912825, 9811875
Infectious Mononucleosis	Associate	11493483, 11520777, 15195244, 15682426, 19570996, 23944711
Inflammation	Associate	22653875, 24435511, 33987447
Leprosy	Associate	15356162
Leukemia Myelogenous Chronic BCR ABL Positive	Associate	27384990
Leukemia Myeloid Acute	Inhibit	37634081
Light Fixation Seizure Syndrome	Associate	11493483, 15358621
Lung Diseases	Associate	25572984
Lupus Erythematosus Systemic	Associate	22549634, 26221972
Lupus Erythematosus Systemic	Inhibit	27183584
Lymphocytic Choriomeningitis	Associate	25572984
Lymphohistiocytosis Hemophagocytic	Associate	11133747, 11159547, 15677558, 18832568, 23944711, 24985396, 25233452, 27209435, 28196537, 29649976, 31754776, 32542393
Lymphoma	Associate	11159547, 19570996
Lymphoma B Cell	Associate	10691868, 11493483, 23589280, 9811875
Lymphoma T Cell	Associate	17640856, 20207847
Lymphoma T Cell Peripheral	Associate	17640856, 20207847
Lymphoproliferative Disorders	Associate	10549287, 10607564, 10691868, 10814994, 10852966, 10898506, 10934222, 11034354, 11049992, 11133747, 11159547, 11342640, 11389028, 11493483, 11509608 View all (45 more)
Lymphoproliferative Disorders	Inhibit	34987501, 36254040
Lymphoproliferative Syndrome X Linked 2	Associate	24616127, 31754776
Meningoencephalitis	Associate	34987501
Mononeuropathies	Associate	11133747
Mucolipidoses	Associate	1637339
Nasopharyngeal Carcinoma	Associate	37274867
Neoplasm Metastasis	Associate	37858067
Neoplasms	Associate	31817155, 37858067
Paraparesis Tropical Spastic	Stimulate	19997502
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	17640856
Precursor Cell Lymphoblastic Leukemia Lymphoma	Inhibit	31951638
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	19570996, 26785729
Primary Immunodeficiency Diseases	Associate	32081864, 35553639
Progressive hearing loss stapes fixation	Associate	32542393
Scoptophobia	Associate	35972918
Sphingolipidoses	Associate	1371116
Splenomegaly	Associate	29649976
Systemic Inflammatory Response Syndrome	Associate	19997502
Systemic Vasculitis	Associate	11133747, 15682426
Thrombosis	Associate	34987501
Tuberculosis	Associate	24327799
Vasculitis Leukocytoclastic Cutaneous	Associate	34416217

SH2D1A (SH2 domain containing 1A)