SLC44A2

Summary

SLC44A2 (solute carrier family 44 member 2 (CTL2 blood group), HGNC:17292) is a protein-coding gene on chromosome 19p13.2, encoding Choline transporter-like protein 2 (Q8IWA5). Choline/H+ antiporter, mainly in mitochondria.

Enables choline transmembrane transporter activity and ethanolamine transmembrane transporter activity. Involved in choline transport; ethanolamine transport; and transmembrane transport. Located in mitochondrial outer membrane and plasma membrane.

Source: NCBI Gene 57153 — RefSeq curated summary.

At a glance

• GWAS associations: 26
• Clinical variants (ClinVar): 137 total
• MANE Select transcript: NM_020428

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17292
Approved symbol	SLC44A2
Name	solute carrier family 44 member 2 (CTL2 blood group)
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	HNA-3, CTL2
Ensembl gene	ENSG00000129353
Ensembl biotype	protein_coding
OMIM	606106
Entrez	57153

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 14 protein_coding, 4 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000335757, ENST00000407327, ENST00000586078, ENST00000586549, ENST00000588214, ENST00000588393, ENST00000588409, ENST00000588465, ENST00000588688, ENST00000589561, ENST00000590382, ENST00000590475, ENST00000590857, ENST00000591194, ENST00000592293, ENST00000857521, ENST00000857522, ENST00000857523, ENST00000857524, ENST00000857525, ENST00000946363

RefSeq mRNA: 3 — MANE Select: NM_020428 NM_001145056, NM_001363611, NM_020428

CCDS: CCDS12245, CCDS54216, CCDS86700

Canonical transcript exons

ENST00000335757 — 22 exons

Exon	Start	End
ENSE00001133348	10643279	10644557
ENSE00002816130	10625553	10625670
ENSE00003466135	10631275	10631385
ENSE00003467532	10632044	10632156
ENSE00003491222	10637644	10637747
ENSE00003500590	10637856	10637929
ENSE00003521624	10627920	10628004
ENSE00003528788	10631057	10631141
ENSE00003533530	10631868	10631951
ENSE00003535362	10631475	10631535
ENSE00003538591	10634974	10635073
ENSE00003539578	10642367	10642451
ENSE00003544663	10636662	10636756
ENSE00003559198	10631626	10631749
ENSE00003563663	10635163	10635255
ENSE00003573199	10636323	10636585
ENSE00003598318	10638227	10638315
ENSE00003613488	10627722	10627795
ENSE00003617382	10635431	10635515
ENSE00003618492	10638023	10638093
ENSE00003676064	10634756	10634887
ENSE00003681119	10626253	10626301

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 98.70.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 68.6627 / max 885.1107, expressed in 1805 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173814	41.7572	1763
173818	21.4004	1269
173819	1.4300	432
173817	0.5859	330
173824	0.5760	295
173829	0.5527	280
173825	0.5007	230
173816	0.4519	249
173823	0.4064	151
173822	0.3540	192

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibial nerve	UBERON:0001323	98.70	gold quality
right lung	UBERON:0002167	98.58	gold quality
right testis	UBERON:0004534	98.54	gold quality
left testis	UBERON:0004533	98.45	gold quality
spleen	UBERON:0002106	98.34	gold quality
right coronary artery	UBERON:0001625	98.24	gold quality
granulocyte	CL:0000094	98.22	gold quality
popliteal artery	UBERON:0002250	98.22	gold quality
tibial artery	UBERON:0007610	98.22	gold quality
upper lobe of left lung	UBERON:0008952	98.00	gold quality
descending thoracic aorta	UBERON:0002345	97.91	gold quality
left coronary artery	UBERON:0001626	97.90	gold quality
lower esophagus mucosa	UBERON:0035834	97.86	gold quality
aorta	UBERON:0000947	97.85	gold quality
ventricular zone	UBERON:0003053	97.74	gold quality
coronary artery	UBERON:0001621	97.73	gold quality
stromal cell of endometrium	CL:0002255	97.62	gold quality
upper lobe of lung	UBERON:0008948	97.62	gold quality
right lobe of thyroid gland	UBERON:0001119	97.60	gold quality
body of stomach	UBERON:0001161	97.53	gold quality
thoracic aorta	UBERON:0001515	97.49	gold quality
ascending aorta	UBERON:0001496	97.48	gold quality
skin of leg	UBERON:0001511	97.48	gold quality
metanephros cortex	UBERON:0010533	97.42	gold quality
blood	UBERON:0000178	97.40	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.38	gold quality
left lobe of thyroid gland	UBERON:0001120	97.19	gold quality
gastrocnemius	UBERON:0001388	97.13	gold quality
esophagus mucosa	UBERON:0002469	97.12	gold quality
skin of abdomen	UBERON:0001416	97.10	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-5061	yes	25.92
E-ANND-3	yes	12.62
E-MTAB-6386	no	2597.10
E-MTAB-7606	no	1418.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting SLC44A2, 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-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-5692A	100.00	74.40	6850
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085

Literature-anchored findings (GeneRIF, showing 28)

• CTL2 is more widely distributed than previously described, and its prominent expression on cells facing the scala media suggests a possible role in homeostasis. (PMID:17926100)
• SNP with arginine rather than glutamine at position 154 constitutes HNA-3a antigen and risk of transfusion-related acute lung injury (TRALI) (PMID:20037594)
• Mass spectrometric analysis of proteins immunoprecipitated from leukocytes by anti-HNA-3a provided direct evidence that anti-HNA-3a recognizes choline transporter-like protein 2. (PMID:20040764)
• In conclusion, choline transport in A549 cells is increased by treatment with DEX, and the increase is mediated by induction of functional choline transporters CTL1 and CTL2. (PMID:20410607)
• SLC44A2 P1 and P2 isoforms with differing glycosylation are variably expressed in cochlea, tongue, heart, colon, lung, kidney, liver and spleen suggesting tissue specific differences that may influence function in each tissue. (PMID:20665236)
• inherited 537T variant of CTL2 gene is located in HNA-3a allele results impaired granulocyte agglutination by four of 14 antibodies tested while 988T remains nearly unaffected. (PMID:21564101)
• African Americans have a significantly lower probability of possessing the SLC44A2*2 allele and may thus be less likely to form the clinically relevant anti-HNA-3a. (PMID:22040064)
• HEK293 cells expressing full-length CTL2 proteins were useful in the detection of HNA-3 antibodies even in the presence of HLA antibodies. (PMID:22211383)
• HNA-3b/b genotype results for six different racial and ethnic groups showed that there could be a significant risk of producing anti-HNA-3a in Chinese, and Caucasian and Asian Indian blood donors, but low risk in Hispanic, African, or Native Americans. (PMID:22414054)
• Allele frequencies were determined in the blood donor population as follows: 0.318 for HNA-1a, 0.668 for HNA-1b, 0.014 for HNA-1c, 0.768 for HNA-3a, 0.232 for HNA-3b, 0.882 for HNA-4a, 0.118 for HNA-4b, 0.736 for HNA-5a and 0.264 for HNA-5b. (PMID:23398146)
• The findings show that, for binding to CTL2, Type 2 HNA-3a antibodies require nonpolymorphic amino acid residues in the third, and possibly the second, EC loops of CTL2 (PMID:24846273)
• HNA-3a (CTL2) antibodies in the pathogenesis of transfusion-related acute lung injury (PMID:25006121)
• The HNA-3 incompatibility in central Thais (33.28%) was higher than northern Thais (28.75%), corresponding to a significantly higher probability of HNA-3a alloimmunization (P<0.05) similar to Japanese and Chinese populations. This study showed the high risk of HNA-3 incompatibility and alloimmunization, especially in central Thai blood donors. (PMID:25608003)
• Meta-analysis of 65,734 individuals identifies TSPAN15 and SLC44A2 as two susceptibility loci for venous thromboembolism. (PMID:25772935)
• Study found 38 SNPs, including one novel SNP, in 8192 nucleotides covering the CDS of the SLC44A2 gene among 302 blood donors. (PMID:26437811)
• The Yi population of China had the highest frequency of blood donors at risk of harboring anti-HNA-3a compared to any population (PMID:26593331)
• The differential expression pattern of CTL1 and CTL2 suggests that CTL1 is the key transporter involved in choline transport from maternal circulation and both transporters are likely involved in stromal and endothelial cell choline transport. (PMID:26601765)
• Variants in SLC44A2 gene is associated with thrombosis. (PMID:26908601)
• Although circulating nucleosomes and elastase - alpha 1-antitrypsin complexes are at present the best characterized biomarkers for neutrophil extracellular traps formation and neutrophil activation, their lack of association with rs2288904 genotype does not exclude a role for SLC44A2 in neutrophil activation (and possibly NET formation) in Venous Thromboembolism. (PMID:27093231)
• SLC44A2 SNPs are associated with Meniere’s disease severity. (PMID:27829169)
• SLC44A2*01 allele is associated with venous thromboembolism and constitutes a potential marker for recurrent venous thromboembolism among Thai patients. (PMID:30634167)
• Activated alphaIIbbeta3 on platelets mediates flow-dependent NETosis via SLC44A2. (PMID:32314961)
• The Effect of Common Variants in SLC44A2 on the Contribution to the Risk of Deep Cein Thrombosis after Orthopedic Surgery. (PMID:32581188)
• Impaired adhesion of neutrophils expressing Slc44a2/HNA-3b to VWF protects against NETosis under venous shear rates. (PMID:33556175)
• Functional Expression of Choline Transporters in Human Neural Stem Cells and Its Link to Cell Proliferation, Cell Viability, and Neurite Outgrowth. (PMID:33672580)
• Choline transporter-like proteins 1 and 2 are newly identified plasma membrane and mitochondrial ethanolamine transporters. (PMID:33789160)
• Lack of the human choline transporter-like protein SLC44A2 causes hearing impairment and a rare red blood phenotype. (PMID:36695047)
• SLC44A2 regulates vascular smooth muscle cell phenotypic switching and aortic aneurysm. (PMID:38916960)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc44a2	ENSDARG00000037059
		ENSDARG00000103399
mus_musculus	Slc44a2	ENSMUSG00000057193
rattus_norvegicus	Slc44a2	ENSRNOG00000031824

Paralogs (4): SLC44A1 (ENSG00000070214), SLC44A5 (ENSG00000137968), SLC44A3 (ENSG00000143036), SLC44A4 (ENSG00000204385)

Protein

Protein identifiers

Choline transporter-like protein 2 — Q8IWA5 (reviewed: Q8IWA5)

Alternative names: Solute carrier family 44 member 2

All UniProt accessions (9): Q8IWA5, A0A088QCU6, A0A140TA83, K7EMN3, K7EMR2, K7EPV6, K7ER17, K7ESF5, K7ESP7

UniProt curated annotations — full annotation on UniProt →

Function. Choline/H+ antiporter, mainly in mitochondria. Also acts as a low-affinity ethanolamine/H+ antiporter, regulating the supply of extracellular ethanolamine (Etn) for the CDP-Etn pathway, redistribute intracellular Etn and balance the CDP-Cho and CDP-Etn arms of the Kennedy pathway. Does not exhibit choline transporter activity.

Subunit / interactions. Interacts with COCH.

Subcellular location. Cell membrane. Mitochondrion outer membrane.

Tissue specificity. Present in supporting cells of the inner ear (at protein level). Expressed in inner ear vestibular tissue.

Miscellaneous. Produced by alternative promoter usage.

Similarity. Belongs to the CTL (choline transporter-like) family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8IWA5-1	1, CTL2a, CTL2P2A	yes
Q8IWA5-2	2, CTL2b, CTL2P2B
Q8IWA5-3	3, CTL2P1

RefSeq proteins (3): NP_001138528, NP_001350540, NP_065161* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007603	Choline_transptr-like	Family

Pfam: PF04515

Catalyzed reactions (Rhea), 2 shown:

• choline(out) + n H(+)(in) = choline(in) + n H(+)(out) (RHEA:75463)
• ethanolamine(out) + n H(+)(in) = ethanolamine(in) + n H(+)(out) (RHEA:75467)

UniProt features (33 total): topological domain 11, transmembrane region 10, sequence conflict 4, glycosylation site 3, splice variant 2, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IWA5-F1	83.62	0.34

Functional residue map

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

Post-translational modifications (1): 14

Glycosylation sites (3): 187, 200, 417

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-1483191	Synthesis of PC
R-HSA-6798163	Choline catabolism
R-HSA-6798695	Neutrophil degranulation
R-HSA-9958517	SLC-mediated bile acid transport
R-HSA-425366

MSigDB gene sets: 210 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_PHOSPHATIDYLCHOLINE_BIOSYNTHETIC_PROCESS, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, GCANCTGNY_MYOD_Q6, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, CAGCTG_AP4_Q5, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS

GO Biological Process (5): phosphatidylcholine biosynthetic process (GO:0006656), choline transport (GO:0015871), ethanolamine transport (GO:0034229), positive regulation of canonical NF-kappaB signal transduction (GO:0043123), transmembrane transport (GO:0055085)

GO Molecular Function (4): choline transmembrane transporter activity (GO:0015220), antiporter activity (GO:0015297), transmembrane transporter activity (GO:0022857), ethanolamine transmembrane transporter activity (GO:0034228)

GO Cellular Component (7): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), lysosomal membrane (GO:0005765), plasma membrane (GO:0005886), membrane (GO:0016020), specific granule membrane (GO:0035579), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	1
Metabolism of amino acids and derivatives	1
Innate Immune System	1
SLC-mediated transport of organic anions	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phosphatidylcholine metabolic process	1
glycerophospholipid biosynthetic process	1
nitrogen compound transport	1
amine transport	1
organic hydroxy compound transport	1
canonical NF-kappaB signal transduction	1
regulation of canonical NF-kappaB signal transduction	1
positive regulation of intracellular signal transduction	1
transport	1
cellular process	1
choline transport	1
transmembrane transporter activity	1
secondary active transmembrane transporter activity	1
transporter activity	1
transmembrane transport	1
amine transmembrane transporter activity	1
alcohol transmembrane transporter activity	1
ethanolamine transport	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrial membrane	1
organelle outer membrane	1
lysosome	1
lytic vacuole membrane	1
membrane	1
cell periphery	1
cellular anatomical structure	1
secretory granule membrane	1
specific granule	1
extracellular vesicle	1

Protein interactions and networks

STRING

932 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC44A2	COCH	O43405	817
SLC44A2	KEAP1	Q14145	724
SLC44A2	CDKN2D	P55273	671
SLC44A2	TSPAN15	O95858	662
SLC44A2	VWF	P04275	582
SLC44A2	SLC5A7	Q9GZV3	565
SLC44A2	CWC27	Q6UX04	536
SLC44A2	AP3B1	O00203	450
SLC44A2	FGG	P02679	432
SLC44A2	SLC2A1	P11166	418
SLC44A2	CD81	P18582	417
SLC44A2	ITGB3	P05106	412
SLC44A2	CDH23	Q9H251	410
SLC44A2	ITGA2B	P08514	409
SLC44A2	S100A3	P33764	402

IntAct

23 interactions, top by confidence:

A	B	Type	Score
CD9	ADAM10	psi-mi:“MI:0914”(association)	0.750
E	AP3B1	psi-mi:“MI:0914”(association)	0.530
LGALS3	PODXL	psi-mi:“MI:0914”(association)	0.530
SLC44A2	BDKRB1	psi-mi:“MI:0915”(physical association)	0.370
SLC44A2	HTR2B	psi-mi:“MI:0915”(physical association)	0.370
TRPV2	SLC44A2	psi-mi:“MI:0915”(physical association)	0.370
	ESYT2	psi-mi:“MI:0914”(association)	0.350
RP2	QSOX1	psi-mi:“MI:0914”(association)	0.350
TEX101	NDUFA4	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
CD81	STX3	psi-mi:“MI:0914”(association)	0.350
CD81	PVR	psi-mi:“MI:0914”(association)	0.350
ZDHHC12	NBAS	psi-mi:“MI:0914”(association)	0.350
STUM	PLSCR1	psi-mi:“MI:0914”(association)	0.350
LGALS9	LGALS8	psi-mi:“MI:0914”(association)	0.350
RP2	NMT2	psi-mi:“MI:0914”(association)	0.350
SLC44A1	UPK3BL1	psi-mi:“MI:0914”(association)	0.350
SLC44A2	CLGN	psi-mi:“MI:0914”(association)	0.350
SLC52A3	TMEM120B	psi-mi:“MI:0914”(association)	0.350

BioGRID (61): SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Two-hybrid), SLC44A2 (Two-hybrid), SLC44A2 (Affinity Capture-RNA), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS), SLC44A2 (Affinity Capture-MS)

ESM2 similar proteins: A3KMY4, A5D7H3, A5PF08, A5PMW0, B0JZD0, B0S5A7, B4F795, B5TYT3, B5X3W7, F1S584, O54902, P04839, P49282, P52649, P58421, Q3MHV9, Q53GD3, Q5R419, Q5R5L9, Q5XEZ5, Q66IV3, Q68EQ9, Q6AY92, Q6DHB5, Q6DHU1, Q6GN42, Q6INE8, Q6IP59, Q6IR74, Q6MG71, Q6X893, Q7SYC9, Q7T2B0, Q7TNK0, Q810F1, Q8BY89, Q8IWA5, Q8NCS7, Q8VII6, Q8VZM5

Diamond homologs: A3KMY4, A5D7H3, A5PF08, A5PMW0, A8XKF2, B0JZD0, B0S5A7, B4F795, B5X3W7, F1S584, Q20026, Q53GD3, Q54I48, Q5R5L9, Q5RJI2, Q6GN42, Q6IP59, Q6MG71, Q7PRJ0, Q7SYC9, Q7T2B0, Q810F1, Q8BY89, Q8IWA5, Q8NCS7, Q91VA1, Q95JW2, Q9VAP3, Q4I8E9, Q6C938, Q6IR74, Q869R1, Q8N4M1, Q8WWI5, A5PK40, Q6AY92, Q54IJ2, Q9I9B9, Q12412, Q5AB93

SIGNOR signaling

4 interactions.

A	Effect	B	Mechanism
SLC44A2	up-regulates	NfKb-p65/p50
ethanol	“up-regulates quantity”	SLC44A2
KAT2A	“up-regulates quantity”	SLC44A2
SLC44A2	“up-regulates activity”	choline	relocalization

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	94
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2989 predictions. Top by Δscore:

Variant	Effect	Δscore
19:10626298:ATAG:A	donor_gain	1.0000
19:10626302:G:C	donor_loss	1.0000
19:10626302:G:GG	donor_gain	1.0000
19:10627915:CACAG:C	acceptor_loss	1.0000
19:10627916:ACAGC:A	acceptor_loss	1.0000
19:10627917:CAGCC:C	acceptor_loss	1.0000
19:10627918:A:AC	acceptor_loss	1.0000
19:10627918:A:AG	acceptor_gain	1.0000
19:10627918:AGCCT:A	acceptor_gain	1.0000
19:10627919:G:GA	acceptor_gain	1.0000
19:10627919:GC:G	acceptor_gain	1.0000
19:10627919:GCC:G	acceptor_gain	1.0000
19:10627919:GCCT:G	acceptor_gain	1.0000
19:10627919:GCCTG:G	acceptor_gain	1.0000
19:10628000:AACGA:A	donor_gain	1.0000
19:10628001:ACGA:A	donor_gain	1.0000
19:10628001:ACGAG:A	donor_loss	1.0000
19:10628002:CGA:C	donor_gain	1.0000
19:10628003:GA:G	donor_gain	1.0000
19:10628003:GAG:G	donor_gain	1.0000
19:10628004:AG:A	donor_loss	1.0000
19:10628005:G:GG	donor_gain	1.0000
19:10628005:GT:G	donor_loss	1.0000
19:10628006:T:A	donor_loss	1.0000
19:10628007:GAGTT:G	donor_loss	1.0000
19:10631270:CCCAG:C	acceptor_loss	1.0000
19:10631271:CCAGA:C	acceptor_loss	1.0000
19:10631272:CAGA:C	acceptor_loss	1.0000
19:10631273:A:AG	acceptor_gain	1.0000
19:10631273:A:T	acceptor_loss	1.0000

AlphaMissense

4642 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:10626301:G:T	R29M	1.000
19:10627979:T:A	C74S	1.000
19:10627980:G:C	C74S	1.000
19:10637869:G:T	G570V	1.000
19:10627722:G:C	R29S	0.999
19:10627722:G:T	R29S	0.999
19:10627786:G:C	G51R	0.999
19:10627932:G:A	G58E	0.999
19:10627979:T:C	C74R	0.999
19:10627980:G:A	C74Y	0.999
19:10627980:G:T	C74F	0.999
19:10627981:C:G	C74W	0.999
19:10631094:T:A	C95S	0.999
19:10631094:T:C	C95R	0.999
19:10631095:G:C	C95S	0.999
19:10631127:T:A	C106S	0.999
19:10631127:T:C	C106R	0.999
19:10631128:G:C	C106S	0.999
19:10631278:T:A	C112S	0.999
19:10631278:T:C	C112R	0.999
19:10631279:G:A	C112Y	0.999
19:10631279:G:C	C112S	0.999
19:10631280:C:G	C112W	0.999
19:10631290:T:A	C116S	0.999
19:10631290:T:C	C116R	0.999
19:10631291:G:C	C116S	0.999
19:10631360:G:A	C139Y	0.999
19:10631505:T:A	C158S	0.999
19:10631505:T:C	C158R	0.999
19:10631506:G:C	C158S	0.999

dbSNP variants (sampled 300 via entrez): RS1000108234 (19:10608206 G>C), RS1000115013 (19:10629747 A>G,T), RS1000202185 (19:10644282 C>T), RS1000224973 (19:10623182 C>G,T), RS1000281983 (19:10616982 C>G,T), RS1000302724 (19:10638873 C>T), RS1000335395 (19:10617141 T>C), RS1000355546 (19:10639124 G>A), RS1000465528 (19:10633395 C>T), RS1000486787 (19:10611351 C>T), RS1000487865 (19:10614118 A>G), RS1000612786 (19:10617886 C>G,T), RS1000615217 (19:10625285 C>T), RS1000640229 (19:10639933 A>T), RS1000667191 (19:10644570 G>A)

Disease associations

OMIM: gene MIM:606106 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

26 associations (top):

Study	Trait	p-value
GCST002808_3	Venous thromboembolism	3.000000e-15
GCST003390_6	Thrombosis	6.000000e-09
GCST004611_148	High light scatter reticulocyte count	6.000000e-45
GCST004612_95	High light scatter reticulocyte percentage of red cells	3.000000e-44
GCST004616_40	Platelet distribution width	8.000000e-09
GCST004619_189	Reticulocyte fraction of red cells	1.000000e-27
GCST004622_72	Reticulocyte count	6.000000e-27
GCST004628_110	Immature fraction of reticulocytes	6.000000e-41
GCST005531_17	Multiple sclerosis	2.000000e-11
GCST005991_45	Platelet count	2.000000e-09
GCST008103_119	Bipolar disorder	5.000000e-06
GCST008839_587	Height	2.000000e-38
GCST009097_8	Venous thromboembolism	4.000000e-24
GCST90000025_555	Appendicular lean mass	3.000000e-36
GCST90000047_235	Age at first sexual intercourse	2.000000e-08
GCST90002385_493	High light scatter reticulocyte count	1.000000e-79
GCST90002386_63	High light scatter reticulocyte percentage of red cells	4.000000e-80
GCST90002387_41	Immature fraction of reticulocytes	3.000000e-74
GCST90002397_184	Mean spheric corpuscular volume	8.000000e-18
GCST90002401_248	Platelet distribution width	3.000000e-10
GCST90002401_249	Platelet distribution width	6.000000e-09
GCST90002402_614	Platelet count	8.000000e-11
GCST90002405_532	Reticulocyte count	7.000000e-48
GCST90002406_484	Reticulocyte fraction of red cells	3.000000e-50
GCST90020028_1533	Hip circumference adjusted for BMI	2.000000e-10
GCST90020028_1534	Hip circumference adjusted for BMI	7.000000e-11

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0003907	deep vein thrombosis
EFO:0007986	reticulocyte count
EFO:0007984	platelet component distribution width
EFO:0004309	platelet count
EFO:0004980	appendicular lean mass
EFO:0009749	age at first sexual intercourse measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC44 choline transporter-like family

CTD chemical–gene interactions

60 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression	3
bisphenol A	decreases expression, increases expression	2
Arsenic	affects expression, affects methylation	2
Smoke	decreases expression	2
Tobacco Smoke Pollution	affects expression, decreases expression	2
Cyclosporine	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
2,4,6-tribromophenol	increases expression	1
methyleugenol	increases expression	1
triphenyl phosphate	affects expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
decabromobiphenyl ether	increases expression	1
terbufos	increases methylation	1
hydroxyhydroquinone	decreases expression	1
beta-lapachone	increases expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
tetrabromobisphenol A	increases expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
cupric chloride	decreases expression	1
resorcinol	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases expression, affects cotreatment	1
perfluorooctane sulfonic acid	decreases expression	1
lipopolysaccharide, E. coli O26-B6	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
bisphenol S	increases expression	1
jinfukang	affects cotreatment, increases expression	1

Cellosaurus cell lines

6 cell lines: 4 cancer cell line, 2 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_C0UR	HEK293T HNA-3aa	Transformed cell line	Female
CVCL_C0US	HEK293T HNA-3bb	Transformed cell line	Female
CVCL_D4P6	HCT116-SLC44A2-KO-c1	Cancer cell line	Male
CVCL_D4P7	HCT116-SLC44A2-KO-c2	Cancer cell line	Male
CVCL_TN76	HAP1 SLC44A2 (-) 1	Cancer cell line	Male
CVCL_TN77	HAP1 SLC44A2 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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