CD1C

Summary

CD1C (CD1c molecule, HGNC:1636) is a protein-coding gene on chromosome 1q23.1, encoding T-cell surface glycoprotein CD1c (P29017). Antigen-presenting protein that binds self and non-self lipid and glycolipid antigens and presents them to T-cell receptors on natural killer T-cells.

This gene encodes a member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene is broadly distributed throughout the endocytic system via a tyrosine-based motif in the cytoplasmic tail. Alternatively spliced transcript variants of this gene have been observed, but their full-length nature is not known.

Source: NCBI Gene 911 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001765

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1636
Approved symbol	CD1C
Name	CD1c molecule
Location	1q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000158481
Ensembl biotype	protein_coding
OMIM	188340
Entrez	911

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000368170, ENST00000443761

RefSeq mRNA: 1 — MANE Select: NM_001765 NM_001765

CCDS: CCDS1175

Canonical transcript exons

ENST00000368170 — 6 exons

Exon	Start	End
ENSE00001039168	158293212	158293302
ENSE00001731945	158293455	158294774
ENSE00001815946	158289923	158290125
ENSE00002329986	158291134	158291400
ENSE00002332786	158292596	158292874
ENSE00002360420	158292084	158292365

Expression profiles

Bgee: expression breadth ubiquitous, 181 present calls, max score 96.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.8179 / max 311.6581, expressed in 179 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5842	1.3131	155
5849	0.1776	36
5839	0.1052	31
5840	0.0497	21
5848	0.0496	13
5843	0.0462	15
5841	0.0323	9
5845	0.0209	8
5844	0.0083	4
5846	0.0068	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
thymus	UBERON:0002370	96.24	gold quality
granulocyte	CL:0000094	90.92	gold quality
diaphragm	UBERON:0001103	89.14	gold quality
upper leg skin	UBERON:0004262	87.91	gold quality
type B pancreatic cell	CL:0000169	87.37	gold quality
olfactory bulb	UBERON:0002264	86.97	gold quality
leukocyte	CL:0000738	86.90	gold quality
spleen	UBERON:0002106	86.88	gold quality
epithelium of nasopharynx	UBERON:0001951	86.85	gold quality
monocyte	CL:0000576	86.76	gold quality
mononuclear cell	CL:0000842	86.70	gold quality
lymph node	UBERON:0000029	85.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.81	gold quality
vermiform appendix	UBERON:0001154	84.47	gold quality
cervix squamous epithelium	UBERON:0006922	81.72	gold quality
caecum	UBERON:0001153	81.25	gold quality
epithelial cell of pancreas	CL:0000083	80.82	silver quality
hair follicle	UBERON:0002073	80.43	gold quality
skin of hip	UBERON:0001554	80.14	gold quality
upper arm skin	UBERON:0004263	80.14	gold quality
mucosa of urinary bladder	UBERON:0001259	79.06	gold quality
gall bladder	UBERON:0002110	78.67	gold quality
squamous epithelium	UBERON:0006914	78.15	gold quality
rectum	UBERON:0001052	77.91	gold quality
blood	UBERON:0000178	77.66	gold quality
gingival epithelium	UBERON:0001949	77.63	silver quality
esophagus squamous epithelium	UBERON:0006920	77.09	gold quality
parietal pleura	UBERON:0002400	77.05	gold quality
superficial temporal artery	UBERON:0001614	76.87	gold quality
epithelium of esophagus	UBERON:0001976	76.35	gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-MTAB-9801	yes	920.07
E-MTAB-8530	yes	691.57
E-HCAD-32	yes	342.32
E-HCAD-1	yes	52.68
E-HCAD-10	yes	36.93
E-MTAB-6701	yes	26.96
E-MTAB-10042	yes	18.23
E-CURD-112	yes	17.07
E-MTAB-8410	yes	16.23
E-MTAB-6678	yes	10.03
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

79 targeting CD1C, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-4802-3P	99.72	70.13	1273

Literature-anchored findings (GeneRIF, showing 39)

• B cell chronic lymphocytic leukemia cells significantly down-regulated transcripts from CD1c and CD1d genes, permitting cells to evade the immune response (PMID:12454749)
• CD1b and CD1c show strong binding of nitrobenzoxadiazole (NBD)-labeled dialkyl-based ligands. (PMID:14551186)
• CD1c expression was detected on monocytes in the majority of sickle cell anemia patients, and was highly expressed in Sbeta thalassemia patients. (PMID:15556687)
• hypothesis that CD1-restricted T cells might be activated and home to target tissues involved in Hashimoto’s thyroiditis and Graves’ disease (PMID:15749918)
• identified CD1a-, CD1b-, and CD1c-restricted T cells from normal human donors that induce cytolysis and secrete copious IFN-gamma in response to self-CD1 expressed on monocyte-derived dendritic cells (PMID:16272286)
• HCMV encodes multiple blocking strategies targeting group 1 CD1 molecules CD1a, CD1b, and CD1c (PMID:18287231)
• monocyte-derived DCs cultured in an immunoglobulin-rich milieu expressed CD1d but not CD1a, CD1b, and CD1c, whereas DCs cultured in the presence of low levels of immunoglobulins had an opposite CD1 profile (PMID:18337560)
• Microsomal triglyceride transfer protein regulates endogenous and exogenous antigen presentation by group 1 CD1 molecules. (PMID:18624350)
• Data show that CD1c represents the second member of the CD1 family to present lipopeptides. (PMID:19468063)
• CD1c+ myeloid dendritic cells were increased in idiopathic pulmonary fibrosis patients versus controls. (PMID:19556741)
• A model of CD1c with bound mannosyl-beta(1)-phosphomycoketide was constructed and analyzed through molecular dynamics simulations. (PMID:19828201)
• Expression of dendritic cell markers CD11c/BDCA-1 and CD123/BDCA-2 in coronary artery disease upon activation in whole blood. (PMID:20888334)
• Accumulation of BDCA-1 and BDCA-2 around neovessels showed that mDCs and pDCs are recruited to advanced arteriosclerotic plaques. (PMID:21436634)
• both CD1d and CD1c are upregulated by retinoic acid receptor alpha signaling in human B cells (PMID:21451111)
• Identification of self-lipids presented by CD1c and CD1d proteins. (PMID:21900247)
• Escherichia coli-activated CD1c(+) dendritic cells suppressed T-cell proliferation in an IL-10-dependent manner (PMID:22678905)
• Data suggest that when CD1c is up-regulated, ILT4 is recruited to CD1c, thus reducing the inhibitory effect of immunoglobulin-like transcript 4 (ILT4) on CD1d recognition. (PMID:22888216)
• Downregulation of both CD1c and CD1d expression through a Vpu-dependent and Nef-independent mechanism, and the concomitant HIV-1-induced production of host cholesterol decreased the extent of CD1c and CD1d modulation. (PMID:23347583)
• Molecular mechanisms by which CD1c captures distinct classes of self- and mycobacterial antigens are reviewed. Review. (PMID:23468110)
• CD1c-PM complexes stain T cell receptors (TCRs), providing direct evidence for a ternary interaction among CD1c-lipid-TCR. (PMID:23530121)
• for isoforms CD1b through CD1e, our simulations show the near-complete collapse of the hydrophobic cavities in the absence of the antigen. This event results from the spontaneous closure of the binding domain entrance, flanked by two alpha-helices. (PMID:23677998)
• Dysregulated CD1 profile in myeloid dendritic cells in CVID is normalized by IVIg treatment. (PMID:23766460)
• RSV infection induces a distinct pattern of costimulatory molecule expression and cytokine production by BDCA-1(+) and BDCA-3(+) mDCs, and impairs their ability to stimulate T cell proliferation. (PMID:23829893)
• Activated dendritic cell subsets expressing CD141/CLEA9A/CD1c, likely recruited into the tubulointerstitium, are positioned to play a role in the development of fibrosis and, thus, progression to chronic kidney disease. (PMID:24049150)
• [review] Humans express both Group 1 (CD1a, CD1b and CD1c) and Group 2 (CD1d) CD1 molecules with nonredundant functions in response to the presentation of endogenous lipids. (PMID:24556395)
• decidual CD1c(+) dendritic cells with Toxoplasma gondii infection have enhanced cytotoxicity of decidual natural killer cells (PMID:24573986)
• hMPV-infected BDCA-1(+) and BDCA-3(+) mDCs induced expansion of Th17 cells, in response to RSV, BDCA-1(+) mDCs induced expansion of Th1 cells and BDCA-3(+) mDCs induced expansion of Th2 cells and Tregs (PMID:24918929)
• mLPA-specific T cells efficiently kill CD1c(+) acute leukemia cells, poorly recognize nontransformed CD1c-expressing cells, and protect immunodeficient mice against CD1c(+) human leukemia cells. (PMID:24935257)
• There was a significant increase of blood CD1c(+) myeloid dendritic cells in autoimmune uveitis patients. The mature phenotype and function of CD1c(+) mDC1 were regulated by TNFalpha via a p38 MAPK-dependent pathway. (PMID:25784146)
• human CD1c adopts different conformations dependent on ligand occupancy of its groove, with CE and ASG stabilizing CD1c conformations that provide a footprint for binding of CD1c self-reactive T-cell receptors (PMID:26884207)
• Stressed beta-cells have little effect on human BDCA1-expressed dendritic cells activation and function, while enterovirus-infected beta-cells impact these cells significantly. (PMID:26888163)
• these results demonstrated the mechanism that suppression of CD1c by BCG infection is mediated by miR-381-3p (PMID:27296666)
• Circulating atopic dermatitis pre-dendritic CD1c+ cells are premature and bear atopic characteristics even without tissue-specific stimulation, suggesting that their development is not only influenced by the skin microenvironment, but also by the local milieu in the blood. (PMID:27701668)
• We found a significant difference in the density of intraepidermal CD1c+ cells between the examined lesions; the mean CD1c cell count was 7.00/mm(2) for invasive melanomas, 2.94 for in situ melanomas, and 13.35 for dysplastic nevi (PMID:28331853)
• The expression of histones, small nucleolar RNA H/ACA box (SNORA) and small nucleolar RNA C/D/box (SNORD), and long non-coding RNA (lncRNA) is also substantially upregulated in the DCs from aged. In contrast, the antigen-presenting and energy generating pathways are downregulated (PMID:29718193)
• Animal models for human group 1 CD1 protein function. (PMID:33384157)
• Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells. (PMID:34536421)
• CD1C is associated with breast cancer prognosis and immune infiltrates. (PMID:36755259)
• Identifying CD1c as a potential biomarker by the comprehensive exploration of tumor mutational burden and immune infiltration in diffuse large B cell lymphoma. (PMID:38099311)

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
danio_rerio	mhc1laa	ENSDARG00000016056
danio_rerio	mhc1lba	ENSDARG00000016227
danio_rerio	mhc1lda	ENSDARG00000023203
danio_rerio		ENSDARG00000051710
danio_rerio		ENSDARG00000051711
danio_rerio	mhc1lfa	ENSDARG00000051712
danio_rerio	mhc1lga	ENSDARG00000051713
danio_rerio	mhc1lca	ENSDARG00000055813
danio_rerio	mhc1lja	ENSDARG00000096830
danio_rerio	si:dkey-52p2.5	ENSDARG00000096940
danio_rerio	mhc1lla	ENSDARG00000096977

Paralogs (22): HFE (ENSG00000010704), FCGRT (ENSG00000104870), ULBP1 (ENSG00000111981), ULBP2 (ENSG00000131015), ULBP3 (ENSG00000131019), MR1 (ENSG00000153029), RAET1L (ENSG00000155918), CD1D (ENSG00000158473), CD1A (ENSG00000158477), CD1B (ENSG00000158485), CD1E (ENSG00000158488), AZGP1 (ENSG00000160862), RAET1E (ENSG00000164520), RAET1G (ENSG00000203722), MICB (ENSG00000204516), MICA (ENSG00000204520), HLA-C (ENSG00000204525), HLA-E (ENSG00000204592), HLA-G (ENSG00000204632), HLA-F (ENSG00000204642), HLA-A (ENSG00000206503), HLA-B (ENSG00000234745)

Protein

Protein identifiers

T-cell surface glycoprotein CD1c — P29017 (reviewed: P29017)

All UniProt accessions (2): P29017, H0Y6Y6

UniProt curated annotations — full annotation on UniProt →

Function. Antigen-presenting protein that binds self and non-self lipid and glycolipid antigens and presents them to T-cell receptors on natural killer T-cells.

Subunit / interactions. Heterodimer with B2M (beta-2-microglobulin).

Subcellular location. Cell membrane. Endosome membrane. Lysosome.

Tissue specificity. Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues.

Miscellaneous. During protein synthesis and maturation, CD1 family members bind endogenous lipids that are replaced by lipid or glycolipid antigens when the proteins are internalized and pass through endosomes or lysosomes, before trafficking back to the cell surface.

RefSeq proteins (1): NP_001756* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003597	Ig_C1-set	Domain
IPR007110	Ig-like_dom	Domain
IPR011161	MHC_I-like_Ag-recog	Domain
IPR011162	MHC_I/II-like_Ag-recog	Homologous_superfamily
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR037055	MHC_I-like_Ag-recog_sf	Homologous_superfamily
IPR050208	MHC_class-I_related	Family

Pfam: PF07654, PF16497

UniProt features (43 total): strand 18, helix 6, glycosylation site 4, disulfide bond 2, sequence variant 2, sequence conflict 2, topological domain 2, turn 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, short sequence motif 1

Structure

Experimental structures (PDB)

10 structures.

PDB	Method	Resolution (Å)
7MX4	X-RAY DIFFRACTION	1.73
7MXF	X-RAY DIFFRACTION	2
9QWJ	X-RAY DIFFRACTION	2.04
7MXH	X-RAY DIFFRACTION	2.11
9QWK	X-RAY DIFFRACTION	2.27
5C9J	X-RAY DIFFRACTION	2.4
3OV6	X-RAY DIFFRACTION	2.5
4ONO	X-RAY DIFFRACTION	2.71
6C09	X-RAY DIFFRACTION	2.95
6C15	X-RAY DIFFRACTION	3.21

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P29017-F1	88.90	0.76

Functional residue map

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

Disulfide bonds (2): 120–185, 225–280

Glycosylation sites (4): 146, 38, 70, 75

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-1280218	Adaptive Immune System
R-HSA-168256	Immune System

MSigDB gene sets: 211 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, WALLACE_PROSTATE_CANCER_RACE_UP, GOBP_POSITIVE_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, YAGI_AML_WITH_INV_16_TRANSLOCATION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_T_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, MODULE_64, GOCC_CELL_SURFACE, GOBP_LEUKOCYTE_MEDIATED_CYTOTOXICITY, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION_VIA_MHC_CLASS_IB, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, PUJANA_CHEK2_PCC_NETWORK, GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_POSITIVE_REGULATION_OF_T_CELL_MEDIATED_CYTOTOXICITY

GO Biological Process (7): positive regulation of T cell mediated cytotoxicity (GO:0001916), adaptive immune response (GO:0002250), T cell activation involved in immune response (GO:0002286), immune response (GO:0006955), antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006), antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007), immune system process (GO:0002376)

GO Molecular Function (6): endogenous lipid antigen binding (GO:0030883), exogenous lipid antigen binding (GO:0030884), glycolipid binding (GO:0051861), lipopeptide binding (GO:0071723), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (10): obsolete extracellular space (GO:0005615), lysosome (GO:0005764), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), endosome membrane (GO:0010008), endosome (GO:0005768), endomembrane system (GO:0012505), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Adaptive Immune System	1
Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
endomembrane system	3
immune response	2
antigen processing and presentation of lipid antigen via MHC class Ib	2
lipid antigen binding	2
lipid binding	2
binding	2
cytoplasm	2
intracellular membrane-bounded organelle	2
plasma membrane	2
cellular anatomical structure	2
positive regulation of leukocyte mediated cytotoxicity	1
T cell mediated cytotoxicity	1
regulation of T cell mediated cytotoxicity	1
positive regulation of T cell mediated immunity	1
lymphocyte activation involved in immune response	1
T cell activation	1
immune system process	1
response to stimulus	1
antigen processing and presentation of endogenous antigen	1
antigen processing and presentation of exogenous antigen	1
biological_process	1
carbohydrate derivative binding	1
lytic vacuole	1
membrane	1
cell periphery	1
cell surface	1
side of membrane	1
endosome	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
cytoplasmic vesicle	1
vacuole	1

Protein interactions and networks

STRING

2308 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CD1C	CD83	Q01151	937
CD1C	CD207	Q9UJ71	919
CD1C	CLEC4C	Q8WTT0	914
CD1C	B2M	P01884	899
CD1C	THBD	P07204	890
CD1C	CD68	P34810	883
CD1C	CD4	P01730	879
CD1C	ITGAX	P20702	879
CD1C	IL3RA	P26951	870
CD1C	CD209	Q9NNX6	853
CD1C	CD8A	P01732	843
CD1C	CD86	P42081	812
CD1C	CD2	P06729	807
CD1C	IL10	P22301	807
CD1C	CD80	P33681	797

IntAct

9 interactions, top by confidence:

A	B	Type	Score
CD1C	ATXN10	psi-mi:“MI:0915”(physical association)	0.560
CD1C	JPH3	psi-mi:“MI:0915”(physical association)	0.560
CD1C		psi-mi:“MI:0915”(physical association)	0.000
	CD1C	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: O35799, O62848, P01898, P01899, P06126, P06339, P10321, P11609, P11610, P13747, P13752, P13753, P14429, P14430, P15812, P15813, P15978, P16212, P16215, P17693, P23043, P29016, P29017, P30511, P30515, P30516, P30517, P60018, P70387, Q28565, Q29422, Q30201, Q3ZCH5, Q4ACW4, Q5YB65, Q63493, Q95IT1, Q95IT3, Q9GKZ0, Q9GL41

Diamond homologs: C1ITJ8, O19477, O35799, P01888, P01889, P01893, P01894, P01895, P01896, P01897, P01898, P01899, P01900, P01901, P01902, P03991, P04223, P04439, P06126, P06140, P06339, P10321, P13747, P13748, P13749, P13750, P13751, P13752, P13753, P13765, P14426, P14427, P14428, P14429, P14430, P14431, P14432, P15464, P15978, P15979

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

803 predictions. Top by Δscore:

Variant	Effect	Δscore
1:158291108:A:AG	acceptor_gain	1.0000
1:158291396:GAAAT:G	donor_gain	1.0000
1:158291401:G:GG	donor_gain	1.0000
1:158291106:A:AG	acceptor_gain	0.9900
1:158291109:C:G	acceptor_gain	0.9900
1:158291397:AAAT:A	donor_gain	0.9900
1:158291398:AAT:A	donor_gain	0.9900
1:158291398:AATGT:A	donor_loss	0.9900
1:158291399:AT:A	donor_gain	0.9900
1:158291399:ATGTA:A	donor_loss	0.9900
1:158291400:TG:T	donor_loss	0.9900
1:158291401:GT:G	donor_loss	0.9900
1:158291402:TAAG:T	donor_loss	0.9900
1:158292594:A:AG	acceptor_gain	0.9900
1:158292595:G:GG	acceptor_gain	0.9900
1:158292595:GTGA:G	acceptor_gain	0.9900
1:158290153:TTAC:T	donor_gain	0.9800
1:158291107:C:G	acceptor_gain	0.9800
1:158291111:A:AG	acceptor_gain	0.9800
1:158291111:ACTT:A	acceptor_gain	0.9800
1:158291129:A:AG	acceptor_gain	0.9800
1:158292079:TCCA:T	acceptor_loss	0.9800
1:158292083:G:GA	acceptor_loss	0.9800
1:158292593:CAGTG:C	acceptor_gain	0.9800
1:158292594:AGTGA:A	acceptor_gain	0.9800
1:158292595:GT:G	acceptor_gain	0.9800
1:158292595:GTGAG:G	acceptor_gain	0.9800
1:158290155:ACAT:A	donor_gain	0.9700
1:158291112:C:G	acceptor_gain	0.9700
1:158291127:C:G	acceptor_gain	0.9700

AlphaMissense

2174 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:158292673:T:C	F230L	0.986
1:158292675:C:A	F230L	0.986
1:158292675:C:G	F230L	0.986
1:158292702:G:C	W239C	0.968
1:158292702:G:T	W239C	0.968
1:158292658:T:A	C225S	0.963
1:158292659:G:C	C225S	0.963
1:158292200:T:A	W149R	0.960
1:158292200:T:C	W149R	0.960
1:158292841:A:C	S286R	0.959
1:158292843:T:A	S286R	0.959
1:158292843:T:G	S286R	0.959
1:158292837:C:A	H284Q	0.957
1:158292837:C:G	H284Q	0.957
1:158292823:T:A	C280S	0.956
1:158292824:G:C	C280S	0.956
1:158292674:T:C	F230S	0.944
1:158292674:T:G	F230C	0.942
1:158292700:T:A	W239R	0.942
1:158292700:T:C	W239R	0.942
1:158292658:T:C	C225R	0.936
1:158292659:G:A	C225Y	0.936
1:158292660:T:G	C225W	0.936
1:158292836:A:G	H284R	0.927
1:158291211:T:C	S47P	0.926
1:158291244:T:A	W58R	0.926
1:158291244:T:C	W58R	0.926
1:158291178:T:C	F36L	0.925
1:158291180:T:A	F36L	0.925
1:158291180:T:G	F36L	0.925

dbSNP variants (sampled 300 via entrez): RS1000976741 (1:158291777 C>T), RS1001814127 (1:158294709 C>G), RS1002875977 (1:158288138 G>A), RS1003177926 (1:158293628 G>A,T), RS1003183281 (1:158289930 C>T), RS1003888556 (1:158293408 C>T), RS1004160489 (1:158291557 C>G,T), RS1005150918 (1:158292129 G>A,T), RS1005258347 (1:158292533 G>A,C,T), RS1005482700 (1:158289452 G>A), RS1006171794 (1:158294005 A>T), RS1007149448 (1:158288090 T>C), RS1008560153 (1:158291761 C>T), RS1009819027 (1:158290257 C>G,T), RS1010114637 (1:158289946 G>A,T)

Disease associations

OMIM: gene MIM:188340 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009269_21	Dental caries (decayed and filled deciduous teeth)	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
nickel sulfate	increases expression	1
2,3,4,7,8-pentachlorodibenzofuran	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
gadodiamide	increases expression	1
CGP 52608	affects binding, increases reaction	1
Air Pollutants	increases abundance, increases expression	1
Allergens	increases expression	1
Amphotericin B	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Hydralazine	affects cotreatment, increases expression	1
Lipopolysaccharides	affects cotreatment, decreases expression	1
Nickel	increases expression	1
Ozone	increases abundance, increases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Valproic Acid	affects cotreatment, increases expression	1
Vitamin E	increases expression	1
Zidovudine	affects cotreatment, decreases expression	1
Antirheumatic Agents	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B0Z5	Abcam Jurkat CD1C KO	Cancer cell line	Male

Clinical trials (associated diseases)

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