HSH2D

gene
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Also known as ALXHSH2FLJ14886

Summary

HSH2D (hematopoietic SH2 domain containing, HGNC:24920) is a protein-coding gene on chromosome 19p13.11, encoding Hematopoietic SH2 domain-containing protein (Q96JZ2). May be a modulator of the apoptotic response through its ability to affect mitochondrial stability.

T-cell activation requires 2 signals: recognition of antigen by the T-cell receptor (see TCR; MIM 186880) and a costimulatory signal provided primarily by CD28 (MIM 186760) in naive T cells. HSH2 is a target of both of these signaling pathways (Greene et al., 2003 [PubMed 12960172]).

Source: NCBI Gene 84941 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 40 total
  • MANE Select transcript: NM_001382417

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24920
Approved symbolHSH2D
Namehematopoietic SH2 domain containing
Location19p13.11
Locus typegene with protein product
StatusApproved
AliasesALX, HSH2, FLJ14886
Ensembl geneENSG00000196684
Ensembl biotypeprotein_coding
OMIM608349
Entrez84941

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 4 nonsense_mediated_decay, 1 retained_intron

ENST00000535834, ENST00000586872, ENST00000591154, ENST00000593031, ENST00000613195, ENST00000613986, ENST00000616070, ENST00000616645, ENST00000874628, ENST00000912672

RefSeq mRNA: 6 — MANE Select: NM_001382417 NM_001352265, NM_001352266, NM_001369808, NM_001369809, NM_001382417, NM_032855

CCDS: CCDS74304

Canonical transcript exons

ENST00000613986 — 6 exons

ExonStartEnd
ENSE000028925031614368516143774
ENSE000034738491615304316153208
ENSE000034759791615439916154491
ENSE000034762651614872416148875
ENSE000035751541615255216152641
ENSE000037116611615721016158575

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 97.87.

FANTOM5 (CAGE): breadth broad, TPM avg 10.8697 / max 705.8619, expressed in 564 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
17438810.8697564

Top tissues by expression

240 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009497.87gold quality
bone marrow cellCL:000209294.89gold quality
leukocyteCL:000073893.42gold quality
monocyteCL:000057693.36gold quality
vermiform appendixUBERON:000115492.82gold quality
spleenUBERON:000210692.74gold quality
bloodUBERON:000017892.14gold quality
lymph nodeUBERON:000002989.62gold quality
mucosa of transverse colonUBERON:000499186.69gold quality
rectumUBERON:000105286.19gold quality
small intestine Peyer’s patchUBERON:000345486.13gold quality
caecumUBERON:000115384.23gold quality
bone marrowUBERON:000237183.43gold quality
small intestineUBERON:000210883.05gold quality
gall bladderUBERON:000211080.75gold quality
transverse colonUBERON:000115779.83gold quality
minor salivary glandUBERON:000183078.14gold quality
upper lobe of left lungUBERON:000895277.81gold quality
right uterine tubeUBERON:000130277.59gold quality
tonsilUBERON:000237277.48gold quality
body of stomachUBERON:000116177.09gold quality
olfactory segment of nasal mucosaUBERON:000538676.84gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047376.51gold quality
upper lobe of lungUBERON:000894875.94gold quality
body of pancreasUBERON:000115075.59gold quality
mouth mucosaUBERON:000372974.75gold quality
stomachUBERON:000094574.46gold quality
right lungUBERON:000216774.01gold quality
colonic epitheliumUBERON:000039773.93gold quality
saliva-secreting glandUBERON:000104473.69gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-MTAB-9067yes326.74
E-HCAD-6yes140.53
E-MTAB-8410yes25.51
E-ANND-3yes24.41
E-HCAD-11yes18.34
E-CURD-112yes11.80
E-MTAB-10553yes8.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting HSH2D, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-185-3P99.9567.011743
HSA-MIR-391099.9571.132227
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-153-5P99.8973.866317
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-450299.6566.991021
HSA-MIR-568399.3668.592083
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-1227-5P98.6565.321549
HSA-MIR-676-5P98.4968.871492
HSA-MIR-6784-3P98.3964.88662
HSA-MIR-569198.2367.021335
HSA-MIR-6805-3P98.2367.021334
HSA-MIR-6862-3P97.9264.86531
HSA-MIR-1288-3P96.8666.95536
HSA-MIR-10392-3P88.7961.83122

Literature-anchored findings (GeneRIF, showing 10)

  • involved in tyrosine kinase signaling in hematopoietic cells (PMID:11700021)
  • ALX is an adaptor involved in T cell activation and interleukin-2 (IL-2) promoter activation (PMID:12960172)
  • the ALX SH2 domain plays a critical role in ALX function downstream of CD28 (PMID:15284240)
  • ALX exerts its effect on IL-2 up-regulation in the cytoplasm and responds to TCR and CD28 signaling (PMID:16169852)
  • results indicate that RvD1 specifically interacts with both ALX and GPR32 on phagocytes. (PMID:20080636)
  • although ALX is inducibly phosphorylated upon TCR/CD28 stimulation, this phosphorylation is not required for ALX to inhibit T cell activation. (PMID:20471366)
  • LXA decreased IgM and IgG production on activated human B cells through ALX/FPR2-dependent signaling. (PMID:24166736)
  • pro-inflammatory stimuli lead to FPR2/ALX expression while LXA4 induces an anti-inflammatory response (PMID:26248046)
  • Both ALX and ChemR23 were present in human synovium and medial tibial plateau bone obtained following total knee replacement surgery for osteoarthritis. (PMID:27860453)
  • HSH2D contributes to methotrexate resistance in human Tcell acute lymphoblastic leukaemia. (PMID:33000278)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriozgc:92242ENSDARG00000029443
danio_reriohsh2dENSDARG00000042908
mus_musculusHsh2dENSMUSG00000062007
rattus_norvegicusHsh2dENSRNOG00000023614
caenorhabditis_elegansWBGENE00008733

Paralogs (4): SH2D2A (ENSG00000027869), SH2D4A (ENSG00000104611), SH2D4B (ENSG00000178217), SH2D7 (ENSG00000183476)

Protein

Protein identifiers

Hematopoietic SH2 domain-containing proteinQ96JZ2 (reviewed: Q96JZ2)

Alternative names: Adaptor in lymphocytes of unknown function X

All UniProt accessions (6): A0A087WT88, A0A087X0V9, Q96JZ2, K7EP18, K7ER77, K7ES08

UniProt curated annotations — full annotation on UniProt →

Function. May be a modulator of the apoptotic response through its ability to affect mitochondrial stability. Adapter protein involved in tyrosine kinase and CD28 signaling. Seems to affect CD28-mediated activation of the RE/AP element of the interleukin-2 promoter.

Subunit / interactions. Interacts with FES and TNK2.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Predominantly expressed in spleen and hematopoietic cells such as peripheral blood leukocytes and weakly expressed in prostate, thymus, heart, small intestine and placenta.

Post-translational modifications. May be phosphorylated by FES and ACK1.

Isoforms (2)

UniProt IDNamesCanonical?
Q96JZ2-11yes
Q96JZ2-22

RefSeq proteins (6): NP_001339194, NP_001339195, NP_001356737, NP_001356738, NP_001369346, NP_116244 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000980SH2Domain
IPR035047HSH2D_SH2Domain
IPR036860SH2_dom_sfHomologous_superfamily

Pfam: PF00017

UniProt features (25 total): mutagenesis site 7, strand 7, compositionally biased region 3, helix 2, region of interest 2, chain 1, domain 1, sequence conflict 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2CS0SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96JZ2-F162.940.19

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (7):

PositionPhenotype
116no change in the ability to inhibit re/ap up-regulation in response to tcr/cd28 stimulation.
135no change in the ability to inhibit re/ap up-regulation in response to tcr/cd28 stimulation.
192–195no change in the ability to inhibit re/ap up-regulation in response to tcr/cd28 stimulation.
341no change in the ability to inhibit re/ap up-regulation in response to tcr/cd28 stimulation.
346–349no change in the ability to inhibit re/ap up-regulation in response to tcr/cd28 stimulation.
10–13no change in the ability to inhibit re/ap up-regulation in response to tcr/cd28 stimulation.
59loss of the ability to inhibit re/ap up-regulation in response to tcr/cd28 stimulation.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 148 (showing top): GOBP_MEMBRANE_DEPOLARIZATION, GOBP_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS, GOZGIT_ESR1_TARGETS_DN, GOBP_REGULATION_OF_LYMPHOCYTE_APOPTOTIC_PROCESS, GOBP_REGULATION_OF_MEMBRANE_DEPOLARIZATION, CAGCTG_AP4_Q5, GOBP_NEGATIVE_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS, GOBP_REGULATION_OF_B_CELL_APOPTOTIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_LYMPHOCYTE_APOPTOTIC_PROCESS, GOBP_LEUKOCYTE_APOPTOTIC_PROCESS, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP, GOBP_REGULATION_OF_MITOCHONDRIAL_MEMBRANE_POTENTIAL, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, GOBP_LYMPHOCYTE_APOPTOTIC_PROCESS, YNGTTNNNATT_UNKNOWN

GO Biological Process (4): negative regulation of B cell apoptotic process (GO:0002903), signal transduction (GO:0007165), T cell activation (GO:0042110), negative regulation of mitochondrial depolarization (GO:0051902)

GO Molecular Function (2): protein-macromolecule adaptor activity (GO:0030674), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membrane-bounded organelle2
cellular anatomical structure2
cytoplasm2
B cell apoptotic process1
regulation of B cell apoptotic process1
negative regulation of lymphocyte apoptotic process1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
lymphocyte activation1
mitochondrial depolarization1
regulation of mitochondrial depolarization1
negative regulation of membrane depolarization1
protein binding1
molecular adaptor activity1
binding1
intracellular anatomical structure1

Protein interactions and networks

STRING

888 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HSH2DFPR2P25090845
HSH2DANXA1P04083837
HSH2DGPR32O75388822
HSH2DTNK2Q07912768
HSH2DCMKLR1Q99788745
HSH2DLTB4RQ15722726
HSH2DALBP02768571
HSH2DCD28P10747536
HSH2DGPR18Q14330528
HSH2DA0A087WTN9A0A087WTN9501
HSH2DCDC42P21181473
HSH2DVWFP04275471
HSH2DIL6RP08887471
HSH2DCD4P01730467
HSH2DKANSL3Q9P2N6464

IntAct

34 interactions, top by confidence:

ABTypeScore
HSH2DTSG101psi-mi:“MI:0915”(physical association)0.560
HSH2DLDHAL6Bpsi-mi:“MI:0915”(physical association)0.490
HSH2DPINK1psi-mi:“MI:0915”(physical association)0.490
HSH2DRBP7psi-mi:“MI:0915”(physical association)0.490
CRKHSH2Dpsi-mi:“MI:0915”(physical association)0.490
HSH2DTSC1psi-mi:“MI:0915”(physical association)0.490
HSH2DPIK3R3psi-mi:“MI:0915”(physical association)0.490
HSH2DCNMDpsi-mi:“MI:0915”(physical association)0.490
HSH2Dpsi-mi:“MI:0915”(physical association)0.490
RBP7HSH2Dpsi-mi:“MI:0915”(physical association)0.490
HSH2DCRKpsi-mi:“MI:0915”(physical association)0.490
TSC1HSH2Dpsi-mi:“MI:0915”(physical association)0.490
PIK3R3HSH2Dpsi-mi:“MI:0915”(physical association)0.490
HSH2Dpsi-mi:“MI:0915”(physical association)0.490
HSH2DARpsi-mi:“MI:0407”(direct interaction)0.440
HSH2DGAB1psi-mi:“MI:0407”(direct interaction)0.440
HSH2DKITpsi-mi:“MI:0407”(direct interaction)0.440
HSH2DMETpsi-mi:“MI:0407”(direct interaction)0.440
HSH2DNSA2psi-mi:“MI:0915”(physical association)0.400
OLIG1HSH2Dpsi-mi:“MI:0915”(physical association)0.370
TNK2HSH2Dpsi-mi:“MI:0915”(physical association)0.370
HSH2DMPP3psi-mi:“MI:0915”(physical association)0.370
HSH2DALKpsi-mi:“MI:0915”(physical association)0.370

BioGRID (30): HSH2D (Two-hybrid), LDHAL6B (Two-hybrid), PPAPDC2 (Two-hybrid), RBP7 (Two-hybrid), LECT1 (Two-hybrid), PIK3R3 (Two-hybrid), PINK1 (Two-hybrid), TSC1 (Two-hybrid), OLIG1 (Two-hybrid), TNK2 (Two-hybrid), FES (Two-hybrid), NSA2 (Affinity Capture-MS), HSH2D (Affinity Capture-MS), HSH2D (Two-hybrid), HSH2D (Reconstituted Complex)

ESM2 similar proteins: A1L3T7, A2CI98, A2CJ06, A2VCK2, D3ZQL6, E1BBG2, M3WHG5, O15037, O43918, O70303, O75333, P48778, P59729, Q32PJ7, Q3KP66, Q3T191, Q5JYT7, Q5T124, Q5U4F0, Q5XIS1, Q6AXX1, Q6VYH9, Q7TSI1, Q80U38, Q8BGT6, Q8BHW9, Q8BWG4, Q8BWQ5, Q8BZ33, Q8BZW2, Q8C0J6, Q8C2K5, Q8CFK6, Q8IV53, Q8IY33, Q8IZW8, Q8K1S6, Q8K330, Q8N3F8, Q8TB24

Diamond homologs: A6NKC9, A6X942, G5ECJ6, O08908, O88834, P03949, P46109, P47941, Q00655, Q08012, Q08CX2, Q56A36, Q5SQS7, Q5U2U2, Q6AYC8, Q6VYH9, Q6YKA8, Q8BI17, Q8UUU2, Q96JZ2, Q9D7V1, Q9H788, Q9NP31, Q9QXK9, P00519, P00520, P00521, P10447, P20936, P29353, P32577, P41239, P41240, P41241, P42684, P50904, P98083, Q03160, Q0IIE2, Q0VBZ0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 19 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Constitutive Signaling by Aberrant PI3K in Cancer548.8×7e-06
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling537.2×9e-06
PIP3 activates AKT signaling525.7×3e-05
Signaling by Receptor Tyrosine Kinases519.9×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

40 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance34
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1463 predictions. Top by Δscore:

VariantEffectΔscore
19:16143626:CCCCA:Cacceptor_loss1.0000
19:16143627:CCCAG:Cacceptor_loss1.0000
19:16143630:AG:Aacceptor_gain1.0000
19:16143631:G:Tacceptor_loss1.0000
19:16143631:GG:Gacceptor_gain1.0000
19:16148872:GAGA:Gdonor_gain1.0000
19:16148874:GA:Gdonor_gain1.0000
19:16148876:G:GGdonor_gain1.0000
19:16152550:AGG:Aacceptor_gain1.0000
19:16152551:GGG:Gacceptor_gain1.0000
19:16152642:G:GGdonor_gain1.0000
19:16153181:G:GTdonor_gain1.0000
19:16154397:A:AGacceptor_gain1.0000
19:16154397:AGAAG:Aacceptor_gain1.0000
19:16154398:G:GGacceptor_gain1.0000
19:16154398:GAAGG:Gacceptor_gain1.0000
19:16154488:GGAG:Gdonor_gain1.0000
19:16154489:G:GTdonor_gain1.0000
19:16154489:GAG:Gdonor_gain1.0000
19:16154489:GAGGT:Gdonor_loss1.0000
19:16154492:G:GCdonor_loss1.0000
19:16154492:G:GGdonor_gain1.0000
19:16154493:T:Adonor_loss1.0000
19:16143630:A:AGacceptor_gain0.9900
19:16143630:AGG:Aacceptor_gain0.9900
19:16143631:G:GAacceptor_gain0.9900
19:16143631:GGG:Gacceptor_gain0.9900
19:16143631:GGGCT:Gacceptor_gain0.9900
19:16143775:GT:Gdonor_loss0.9900
19:16143776:T:Gdonor_loss0.9900

AlphaMissense

2288 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:16152592:T:CF56L0.996
19:16152594:T:AF56L0.996
19:16152594:T:GF56L0.996
19:16148850:T:AW34R0.993
19:16148850:T:CW34R0.993
19:16152607:A:CS61R0.992
19:16152609:T:AS61R0.992
19:16152609:T:GS61R0.992
19:16152556:G:CA44P0.990
19:16157774:T:CF347L0.989
19:16157776:T:AF347L0.989
19:16157776:T:GF347L0.989
19:16148854:T:CF35S0.985
19:16152603:G:CR59S0.985
19:16152603:G:TR59S0.985
19:16148853:T:CF35L0.984
19:16148855:C:AF35L0.984
19:16148855:C:GF35L0.984
19:16152593:T:CF56S0.984
19:16152602:G:TR59M0.984
19:16148802:T:CF18L0.981
19:16148804:T:AF18L0.981
19:16148804:T:GF18L0.981
19:16153064:T:AH79Q0.980
19:16153064:T:GH79Q0.980
19:16152625:T:GY67D0.979
19:16153144:T:AV106D0.979
19:16148852:G:CW34C0.978
19:16148852:G:TW34C0.978
19:16152602:G:CR59T0.978

dbSNP variants (sampled 300 via entrez): RS1000042614 (19:16136411 C>A,T), RS1000476877 (19:16135448 T>C), RS1000521792 (19:16146470 G>A), RS1000581144 (19:16142606 G>C), RS1000674344 (19:16158154 C>A), RS1000749660 (19:16156933 C>A), RS1000759008 (19:16137187 C>T), RS1001212577 (19:16136919 T>C), RS1001275524 (19:16158242 C>G,T), RS1001490429 (19:16140384 C>A), RS1001586315 (19:16146341 G>A), RS1001638712 (19:16146041 A>G), RS1001663927 (19:16134849 G>C), RS1001752474 (19:16151975 C>T), RS1001824029 (19:16140584 G>A)

Disease associations

OMIM: gene MIM:608349 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

StudyTraitp-value
GCST90002390_532Mean corpuscular hemoglobin1.000000e-28
GCST90002392_71Mean corpuscular volume7.000000e-22
GCST90002397_192Mean spheric corpuscular volume2.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004527mean corpuscular hemoglobin

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases expression2
Benzo(a)pyreneaffects methylation2
Estradiolaffects cotreatment, decreases expression2
Nickelincreases expression2
Tobacco Smoke Pollutiondecreases expression, affects expression2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
ethyl-p-hydroxybenzoatedecreases expression1
perfluorooctanoic aciddecreases expression1
benzo(e)pyrenedecreases methylation1
pinostrobinincreases expression1
abrinedecreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Cadmiumdecreases expression1
Calcitriolincreases expression, affects cotreatment1
Drugs, Chinese Herbalincreases expression1
Formaldehydedecreases expression1
Methapyrilenedecreases methylation1
Methotrexateincreases expression1
Methyl Methanesulfonatedecreases expression1
Naphthoquinonesincreases expression1
Smokedecreases expression1
Testosteroneaffects cotreatment, increases expression1
Tretinoinincreases expression1
Aflatoxin B1decreases expression1
Cadmium Chloridedecreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.