CLSTN1

Summary

CLSTN1 (calsyntenin 1, HGNC:17447) is a protein-coding gene on chromosome 1p36.22, encoding Calsyntenin-1 (O94985). Postsynaptic adhesion molecule that binds to presynaptic neurexins to mediate both excitatory and inhibitory synapse formation.

This gene is a member of the calsyntenin family, a subset of the cadherin superfamily. The encoded transmembrane protein, also known as alcadein-alpha, is thought to bind to kinesin-1 motors to mediate the axonal anterograde transport of certain types of vesicle. Amyloid precursor protein (APP) is trafficked via these vesicles and so this protein is being investigated to see how it might contribute to the mechanisms underlying Alzheimer’s disease. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 22883 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 188 total
• MANE Select transcript: NM_001009566

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17447
Approved symbol	CLSTN1
Name	calsyntenin 1
Location	1p36.22
Locus type	gene with protein product
Status	Approved
Aliases	CSTN1, KIAA0911, CDHR12
Ensembl gene	ENSG00000171603
Ensembl biotype	protein_coding
OMIM	611321
Entrez	22883

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 18 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000361311, ENST00000377298, ENST00000435891, ENST00000464286, ENST00000477264, ENST00000650348, ENST00000872284, ENST00000872285, ENST00000872286, ENST00000872287, ENST00000872288, ENST00000872289, ENST00000932458, ENST00000932459, ENST00000932460, ENST00000932461, ENST00000932462, ENST00000932463, ENST00000960689, ENST00000960690, ENST00000960691

RefSeq mRNA: 3 — MANE Select: NM_001009566 NM_001009566, NM_001302883, NM_014944

CCDS: CCDS105, CCDS30580

Canonical transcript exons

ENST00000377298 — 19 exons

Exon	Start	End
ENSE00001149360	9731206	9731390
ENSE00001149378	9733401	9733546
ENSE00001149387	9733972	9734142
ENSE00001149395	9734948	9735174
ENSE00001149402	9735467	9735615
ENSE00001149407	9735885	9736042
ENSE00001149415	9737498	9737554
ENSE00001149423	9741094	9741256
ENSE00001149433	9743884	9744005
ENSE00001149442	9744395	9744643
ENSE00001149450	9749461	9749646
ENSE00001149461	9749764	9749913
ENSE00001149469	9751473	9751681
ENSE00001149476	9755114	9755309
ENSE00001149484	9756481	9756510
ENSE00001149488	9773272	9773394
ENSE00001545302	9823643	9823965
ENSE00001894826	9728926	9730705
ENSE00003565224	9731761	9731896

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 162.2601 / max 2084.2123, expressed in 1823 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
10244	157.2093	1823
10243	4.8574	1456
10239	0.1104	30
10238	0.0828	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
frontal pole	UBERON:0002795	99.60	gold quality
postcentral gyrus	UBERON:0002581	99.53	gold quality
parietal lobe	UBERON:0001872	99.49	gold quality
Brodmann (1909) area 10	UBERON:0013541	99.49	gold quality
paraflocculus	UBERON:0005351	99.45	gold quality
middle temporal gyrus	UBERON:0002771	99.44	gold quality
orbitofrontal cortex	UBERON:0004167	99.44	gold quality
superior frontal gyrus	UBERON:0002661	99.43	gold quality
Brodmann (1909) area 46	UBERON:0006483	99.42	gold quality
cerebellar vermis	UBERON:0004720	99.36	gold quality
right hemisphere of cerebellum	UBERON:0014890	99.35	gold quality
right frontal lobe	UBERON:0002810	99.33	gold quality
cerebellar cortex	UBERON:0002129	99.30	gold quality
cerebellar hemisphere	UBERON:0002245	99.30	gold quality
cerebellum	UBERON:0002037	99.28	gold quality
frontal cortex	UBERON:0001870	99.26	gold quality
Brodmann (1909) area 9	UBERON:0013540	99.21	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	99.19	gold quality
prefrontal cortex	UBERON:0000451	99.18	gold quality
entorhinal cortex	UBERON:0002728	99.12	gold quality
neocortex	UBERON:0001950	99.11	gold quality
lateral nuclear group of thalamus	UBERON:0002736	99.11	gold quality
cerebral cortex	UBERON:0000956	99.03	gold quality
occipital lobe	UBERON:0002021	99.00	gold quality
primary visual cortex	UBERON:0002436	98.97	gold quality
pons	UBERON:0000988	98.95	gold quality
temporal lobe	UBERON:0001871	98.83	gold quality
cingulate cortex	UBERON:0003027	98.80	gold quality
anterior cingulate cortex	UBERON:0009835	98.79	gold quality
telencephalon	UBERON:0001893	98.74	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	61.22
E-HCAD-35	yes	44.63
E-MTAB-7303	no	422.80
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting CLSTN1, 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-4692	100.00	67.32	2066
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3148	99.97	75.06	6478
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-6793-5P	99.97	65.95	758
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-6124	99.87	69.78	3551

Literature-anchored findings (GeneRIF, showing 8)

• Alcadein and amyloid beta-protein precursor regulates FE65-dependent gene transactivation [alcalpha1, alcbeta, alcgamma] (PMID:15037614)
• Phosphorylation of KLC1 at serine 460 modulates binding and trafficking of calsyntenin-1. (PMID:21385839)
• CLSTN1 is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells. (PMID:21555518)
• findings show that calsyntenin-1 is reduced in Alzheimer’s disease brains and that the extent of this reduction correlates with increased amyloid-beta (PMID:22434822)
• Increased plasma p3-alcadein (alc) alpha, evident in the early stages of cognitive impairment, suggests that alc metabolites are useful plasma biomarkers of Alzheimer’s disease. (PMID:22571980)
• Increased plasma p3-Alcalpha35, a major fragment of alcalpha1, may indicate an endophenotype in Alzheimer’s disease patients with progressive cognitive impairment. (PMID:24305499)
• Calsyntenin-1 contributes to the early stages of the hepatitis C virus replication cycle and the formation of the replication complex. (PMID:27221318)
• Results suggests that APP partially compensates for defective Alcalpha in anterograde transport by providing an alternative cargo receptor for kinesin-1. (PMID:29093024)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	clstn1	ENSDARG00000031720
mus_musculus	Clstn1	ENSMUSG00000039953
rattus_norvegicus	Clstn1	ENSRNOG00000016398
drosophila_melanogaster	Cals	FBGN0039928
caenorhabditis_elegans		WBGENE00000403

Paralogs (2): CLSTN3 (ENSG00000139182), CLSTN2 (ENSG00000158258)

Protein

Protein identifiers

Calsyntenin-1 — O94985 (reviewed: O94985)

Alternative names: Alcadein-alpha, Alzheimer-related cadherin-like protein, Non-classical cadherin XB31alpha

All UniProt accessions (3): A0A3B3ITY6, O94985, Q5SR54

UniProt curated annotations — full annotation on UniProt →

Function. Postsynaptic adhesion molecule that binds to presynaptic neurexins to mediate both excitatory and inhibitory synapse formation. Promotes synapse development by acting as a cell adhesion molecule at the postsynaptic membrane, which associates with neurexin-alpha at the presynaptic membrane. Also functions as a cargo in axonal anterograde transport by acting as a molecular adapter that promotes KLC1 association with vesicles. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. As intracellular fragment AlcICD, suppresses APBB1-dependent transactivation stimulated by APP C-terminal intracellular fragment (AICD), most probably by competing with AICD for APBB1-binding. In complex with APBA2 and C99, a C-terminal APP fragment, abolishes C99 interaction with PSEN1 and thus APP C99 cleavage by gamma-secretase, most probably through stabilization of the direct interaction between APBA2 and APP.

Subunit / interactions. Directly interacts with APBA2. Forms a tripartite complex with APBA2 and APP. Interacts with KLC1. Interacts with APBB1; this interaction stabilizes AlcICD metabolism. Interacts with PSEN1.

Subcellular location. Postsynaptic cell membrane. Endoplasmic reticulum membrane. Golgi apparatus membrane. Cell projection. Neuron projection Nucleus.

Tissue specificity. Expressed in the brain and, a lower level, in the heart, skeletal muscle, kidney and placenta. Accumulates in dystrophic neurites around the amyloid core of Alzheimer disease senile plaques (at protein level).

Post-translational modifications. Proteolytically processed under normal cellular conditions. A primary zeta-cleavage generates a large extracellular (soluble) N-terminal domain (sAlc) and a short C-terminal transmembrane fragment (CTF1). A secondary cleavage catalyzed by presenilin gamma-secretase within the transmembrane domain releases the beta-Alc-alpha chain in the extracellular milieu and produces an intracellular fragment (AlcICD). This processing is strongly suppressed in the tripartite complex formed with APBA2 and APP, which seems to prevent the association with PSEN1.

Domain organisation. The cytoplasmic domain binds synaptic Ca(2+).

Similarity. Belongs to the calsyntenin family.

Isoforms (2)

UniProt ID	Names	Canonical?
O94985-1	1, Alcalpha2	yes
O94985-2	2, Alcalpha1

RefSeq proteins (3): NP_001009566, NP_001289812, NP_055759 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002126	Cadherin-like_dom	Domain
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR015919	Cadherin-like_sf	Homologous_superfamily
IPR045588	CLSTN_C	Domain

Pfam: PF00028, PF13385, PF19699

UniProt features (29 total): sequence variant 6, chain 3, glycosylation site 3, sequence conflict 3, compositionally biased region 2, site 2, mutagenesis site 2, topological domain 2, domain 2, signal peptide 1, splice variant 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O94985-F1	77.63	0.49

Functional residue map

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

Catalytic / active sites (2): 824–825 (cleavage); 853–854 (cleavage)

Glycosylation sites (3): 346, 366, 515

Mutagenesis-validated functional residues (2):

Position	Phenotype
913–914	abolishes interaction with apba2.
918	no effect on apba2-binding.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 276 (showing top): GGTGTGT_MIR329, GOBP_SYNAPSE_ASSEMBLY, MAZ_Q6, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_GROWTH, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOCC_CELL_SURFACE, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, SP1_Q2_01

GO Biological Process (8): regulation of cell growth (GO:0001558), cell adhesion (GO:0007155), homophilic cell-cell adhesion (GO:0007156), positive regulation of synaptic transmission (GO:0050806), positive regulation of synapse assembly (GO:0051965), regulation of synapse maturation (GO:0090128), neurotransmitter receptor transport to postsynaptic membrane (GO:0098969), vesicle-mediated transport in synapse (GO:0099003)

GO Molecular Function (5): amyloid-beta binding (GO:0001540), calcium ion binding (GO:0005509), kinesin binding (GO:0019894), X11-like protein binding (GO:0042988), protein binding (GO:0005515)

GO Cellular Component (16): Golgi membrane (GO:0000139), extracellular region (GO:0005576), nucleus (GO:0005634), endoplasmic reticulum membrane (GO:0005789), cell surface (GO:0009986), postsynaptic density (GO:0014069), neuron projection (GO:0043005), postsynaptic membrane (GO:0045211), postsynaptic endosome (GO:0098845), glutamatergic synapse (GO:0098978), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), membrane (GO:0016020), cell projection (GO:0042995), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
intracellular membrane-bounded organelle	3
synapse	2
postsynapse	2
cytoplasm	2
endomembrane system	2
cell growth	1
regulation of growth	1
regulation of cellular component organization	1
cellular process	1
cell-cell adhesion	1
chemical synaptic transmission	1
positive regulation of cell communication	1
positive regulation of signaling	1
modulation of chemical synaptic transmission	1
synapse assembly	1
positive regulation of nervous system development	1
regulation of synapse assembly	1
positive regulation of cell junction assembly	1
regulation of developmental process	1
regulation of synapse organization	1
synapse maturation	1
receptor localization to synapse	1
neurotransmitter receptor transport to plasma membrane	1
regulation of postsynaptic membrane neurotransmitter receptor levels	1
protein localization to postsynaptic membrane	1
establishment of protein localization to postsynaptic membrane	1
vesicle-mediated transport	1
peptide binding	1
metal ion binding	1
cytoskeletal protein binding	1
protein binding	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
asymmetric synapse	1
postsynaptic specialization	1

Protein interactions and networks

STRING

1184 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLSTN1	KLC1	Q07866	960
CLSTN1	KLC4	Q9NSK0	880
CLSTN1	KLC2	Q9H0B6	826
CLSTN1	KLC3	Q6P597	798
CLSTN1	CDH17	Q12864	775
CLSTN1	APBA2	Q99767	709
CLSTN1	APP	P05067	611
CLSTN1	VAMP2	P19065	521
CLSTN1	SMAP1	Q8IYB5	498
CLSTN1	PRNP	P04156	493
CLSTN1	SCIN	Q9Y6U3	490
CLSTN1	SYT1	P21579	487
CLSTN1	EFCAB7	A8K855	480
CLSTN1	LZIC	Q8WZA0	479
CLSTN1	FN1	P02751	474

IntAct

96 interactions, top by confidence:

A	B	Type	Score
CLSTN1	Klc1	psi-mi:“MI:0915”(physical association)	0.680
Klc1	CLSTN1	psi-mi:“MI:0915”(physical association)	0.680
Klc1	CLSTN1	psi-mi:“MI:0403”(colocalization)	0.680
CLSTN1	Klc1	psi-mi:“MI:0407”(direct interaction)	0.680
CA10	WDHD1	psi-mi:“MI:0914”(association)	0.640
SCGB1D1	MANBA	psi-mi:“MI:0914”(association)	0.640
APBA2	CLSTN1	psi-mi:“MI:0407”(direct interaction)	0.610
APBA2	CLSTN1	psi-mi:“MI:0915”(physical association)	0.610
SCGB1D1	FAM234B	psi-mi:“MI:0914”(association)	0.530
DEFA5	NUDT19	psi-mi:“MI:0914”(association)	0.530
APBA3	DUSP11	psi-mi:“MI:0914”(association)	0.530
APBA3	CLSTN1	psi-mi:“MI:0914”(association)	0.530
EDA	AP3B1	psi-mi:“MI:0914”(association)	0.530
GPIHBP1	ADAM10	psi-mi:“MI:0914”(association)	0.530
KLC1	KIF5C	psi-mi:“MI:0914”(association)	0.530
CLSTN1	RNF10	psi-mi:“MI:0915”(physical association)	0.400
CLSTN1	APBB1	psi-mi:“MI:0915”(physical association)	0.400
CLSTN1	TOPBP1	psi-mi:“MI:0915”(physical association)	0.370
CLSTN1	TRIP12	psi-mi:“MI:0915”(physical association)	0.370
CLSTN1	SETDB1	psi-mi:“MI:0915”(physical association)	0.370
CLSTN1	SLK	psi-mi:“MI:0915”(physical association)	0.370
CLSTN1	MCM3AP	psi-mi:“MI:0915”(physical association)	0.370
CLSTN1	BAHCC1	psi-mi:“MI:0915”(physical association)	0.370
PRNP	CARNS1	psi-mi:“MI:0914”(association)	0.350
Mecom	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (137): CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS)

ESM2 similar proteins: A0A292G9J6, A0A8M9PFP2, A1L2K1, A2A863, A7E2Z9, B0S5G3, B5MFE9, F1R520, F7A4A7, F8VQ03, O93449, O94985, P16144, P35447, P53813, P98089, Q08761, Q0V9V5, Q0VCN6, Q28483, Q3ZCN5, Q5R9Q9, Q5RCW9, Q5RD64, Q61592, Q63772, Q64632, Q6DDW2, Q6DFV8, Q6PZE0, Q6Q0N0, Q8BH34, Q8BJD1, Q8CFM6, Q8CIZ8, Q8CJ69, Q8K410, Q8N2E2, Q8N8U9, Q8R553

Diamond homologs: A0A8M9PFP2, B0S5G3, F1R520, O02840, O55111, O88278, O94985, P30944, P33151, P55287, P55288, Q0VCN6, Q14517, Q5DRC8, Q5R9Q9, Q63418, Q6Q0N0, Q6URK6, Q6V1P9, Q86UP0, Q8BNA6, Q8R553, Q8VDA1, Q96JQ0, Q99JH7, Q9BQT9, Q9EPL2, Q9ER65, Q9H4D0, Q9HCU4, Q9NYQ6, Q9R0M0, P55289, Q5DRA8, Q5DRE0, Q6V0I7, Q967F4, Q9UN71, Q9V498, Q9VW71

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 126 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.

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of T cell receptor signaling pathway	5	17.0×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	147
Likely benign	8
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3415 predictions. Top by Δscore:

Variant	Effect	Δscore
1:9730701:TAGGT:T	acceptor_gain	1.0000
1:9730702:AGGT:A	acceptor_gain	1.0000
1:9730703:GGT:G	acceptor_gain	1.0000
1:9730705:TC:T	acceptor_loss	1.0000
1:9730706:C:CC	acceptor_gain	1.0000
1:9730707:T:C	acceptor_loss	1.0000
1:9731200:TCCTA:T	donor_loss	1.0000
1:9731201:CCTAC:C	donor_loss	1.0000
1:9731202:CTAC:C	donor_loss	1.0000
1:9731203:TAC:T	donor_loss	1.0000
1:9731207:T:TA	donor_gain	1.0000
1:9731386:GACGA:G	acceptor_gain	1.0000
1:9731387:ACGA:A	acceptor_gain	1.0000
1:9731388:CGA:C	acceptor_gain	1.0000
1:9731388:CGAC:C	acceptor_gain	1.0000
1:9731389:GA:G	acceptor_gain	1.0000
1:9731390:AC:A	acceptor_loss	1.0000
1:9731391:C:CC	acceptor_gain	1.0000
1:9731392:T:G	acceptor_loss	1.0000
1:9731755:TCCTA:T	donor_loss	1.0000
1:9731756:CCTA:C	donor_loss	1.0000
1:9731757:CTA:C	donor_loss	1.0000
1:9731758:TACCT:T	donor_loss	1.0000
1:9731759:A:C	donor_loss	1.0000
1:9731760:C:CG	donor_loss	1.0000
1:9733396:CTCA:C	donor_loss	1.0000
1:9733397:TCACC:T	donor_loss	1.0000
1:9733398:CA:C	donor_loss	1.0000
1:9733399:A:AC	donor_gain	1.0000
1:9733399:A:T	donor_loss	1.0000

AlphaMissense

6502 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:9731225:A:C	I910S	1.000
1:9731225:A:G	I910T	1.000
1:9731225:A:T	I910N	1.000
1:9751673:A:T	V150D	1.000
1:9730532:C:A	W974C	0.999
1:9730532:C:G	W974C	0.999
1:9730534:A:G	W974R	0.999
1:9730534:A:T	W974R	0.999
1:9731219:A:T	V912D	0.999
1:9731231:A:G	L908P	0.999
1:9731231:A:T	L908Q	0.999
1:9731245:C:A	W903C	0.999
1:9731245:C:G	W903C	0.999
1:9731347:G:C	S869R	0.999
1:9731347:G:T	S869R	0.999
1:9731349:T:G	S869R	0.999
1:9741239:C:A	W458C	0.999
1:9741239:C:G	W458C	0.999
1:9744535:A:G	F365S	0.999
1:9755294:A:G	F87S	0.999
1:9731215:G:C	N913K	0.998
1:9731215:G:T	N913K	0.998
1:9731247:A:G	W903R	0.998
1:9731247:A:T	W903R	0.998
1:9731355:A:G	C867R	0.998
1:9733419:G:C	S803R	0.998
1:9733419:G:T	S803R	0.998
1:9733421:T:G	S803R	0.998
1:9733446:G:C	C794W	0.998
1:9733448:A:G	C794R	0.998

dbSNP variants (sampled 300 via entrez): RS1000007155 (1:9808003 G>A), RS1000011742 (1:9804712 G>T), RS1000028076 (1:9730273 G>A), RS1000039691 (1:9807722 C>T), RS1000070610 (1:9771499 A>G,T), RS1000074912 (1:9784977 T>A,C), RS1000086557 (1:9786382 C>G), RS1000208700 (1:9740530 G>C), RS1000210128 (1:9822527 C>G), RS1000230858 (1:9789335 C>G,T), RS1000265823 (1:9813363 C>G,T), RS1000268175 (1:9760437 G>A), RS1000275024 (1:9776723 C>T), RS1000303319 (1:9822771 G>A), RS1000315658 (1:9802685 C>A,G,T)

Disease associations

OMIM: gene MIM:611321 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, decreases expression, increases abundance, increases expression	3
Valproic Acid	increases expression, increases methylation	3
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
lead acetate	decreases expression, affects cotreatment	1
beta-lapachone	decreases expression	1
afimoxifene	decreases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
aflatoxin B2	decreases methylation	1
beta-methylcholine	affects expression	1
azoxystrobin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
chloropicrin	decreases expression	1
corosolic acid	increases expression	1
pyrimidifen	decreases expression	1
abrine	decreases expression	1
picoxystrobin	decreases expression	1
Arsenic Trioxide	decreases expression	1
Fulvestrant	decreases expression	1
Acetaminophen	increases expression	1
Arsenic	decreases expression, increases abundance, affects cotreatment	1
Benzo(a)pyrene	affects methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Estradiol	decreases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lead	affects splicing, affects expression	1
Manganese	increases abundance, affects cotreatment, decreases expression	1
Methotrexate	affects response to substance	1

Clinical trials (associated diseases)

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