CAPRIN2

Summary

CAPRIN2 (caprin family member 2, HGNC:21259) is a protein-coding gene on chromosome 12p11.21, encoding Caprin-2 (Q6IMN6). Promotes phosphorylation of the Wnt coreceptor LRP6, leading to increased activity of the canonical Wnt signaling pathway.

The protein encoded by this gene may regulate the transport of mRNA. It may play a role in the differentiation of erythroblasts. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 65981 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 177 total
• MANE Select transcript: NM_001385503

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21259
Approved symbol	CAPRIN2
Name	caprin family member 2
Location	12p11.21
Locus type	gene with protein product
Status	Approved
Aliases	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140
Ensembl gene	ENSG00000110888
Ensembl biotype	protein_coding
OMIM	610375
Entrez	65981

Gene structure

Transcript identifiers

Ensembl transcripts: 88 — 67 protein_coding, 14 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000298892, ENST00000395805, ENST00000417045, ENST00000433722, ENST00000454014, ENST00000534897, ENST00000537108, ENST00000537553, ENST00000538387, ENST00000540436, ENST00000540584, ENST00000541765, ENST00000542550, ENST00000543380, ENST00000546129, ENST00000548676, ENST00000553026, ENST00000614865, ENST00000620681, ENST00000684863, ENST00000686317, ENST00000687797, ENST00000688163, ENST00000689016, ENST00000690097, ENST00000690126, ENST00000690233, ENST00000692932, ENST00000694880, ENST00000695326, ENST00000695327, ENST00000695328, ENST00000695329, ENST00000695330, ENST00000695331, ENST00000695369, ENST00000695370, ENST00000695371, ENST00000695372, ENST00000695373, ENST00000695374, ENST00000695398, ENST00000695400, ENST00000695402, ENST00000893342, ENST00000893343, ENST00000893344, ENST00000893345, ENST00000893346, ENST00000893347, ENST00000893348, ENST00000893349, ENST00000893350, ENST00000893351, ENST00000893352, ENST00000893353, ENST00000921374, ENST00000921375, ENST00000921376, ENST00000921377, ENST00000921378, ENST00000921379, ENST00000921380, ENST00000921381, ENST00000921382, ENST00000921383, ENST00000921384, ENST00000954204, ENST00000954205, ENST00000954206, ENST00000954207, ENST00000954208, ENST00000954209, ENST00000954210, ENST00000954211, ENST00000954212, ENST00000954213, ENST00000954214, ENST00000954215, ENST00000954216, ENST00000954217, ENST00000954218, ENST00000954219, ENST00000954220, ENST00000954221, ENST00000954222, ENST00000954223, ENST00000954224

RefSeq mRNA: 66 — MANE Select: NM_001385503 NM_001002259, NM_001206856, NM_001319842, NM_001319843, NM_001319844, NM_001319845, NM_001319846, NM_001385498, NM_001385499, NM_001385500, NM_001385501, NM_001385502, NM_001385503, NM_001385504, NM_001385505, NM_001385506, NM_001385507, NM_001385508, NM_001385509, NM_001385510, NM_001385511, NM_001385512, NM_001385513, NM_001385514, NM_001385515, NM_001385516, NM_001385518, NM_001385519, NM_001385520, NM_001385521, NM_001385522, NM_001385523, NM_001385524, NM_001385525, NM_001385526, NM_001385527, NM_001385528, NM_001385529, NM_001385531, NM_001385532, NM_001385533, NM_001385534, NM_001385535, NM_001385537, NM_001385538, NM_001385539, NM_001385540, NM_001385541, NM_001385542, NM_001385543, NM_001385544, NM_001385545, NM_001385546, NM_001385547, NM_001385548, NM_001385549, NM_001385550, NM_001385551, NM_001385552, NM_001385553, NM_001385554, NM_001385557, NM_001385559, NM_001416513, NM_023925, NM_032156

CCDS: CCDS41766, CCDS55816, CCDS8720, CCDS91671, CCDS91672, CCDS91675, CCDS91676, CCDS91677, CCDS91678

Canonical transcript exons

ENST00000695402 — 19 exons

Exon	Start	End
ENSE00001759531	30733629	30733711
ENSE00002222354	30753344	30753559
ENSE00002256308	30734968	30735206
ENSE00003466994	30741020	30741106
ENSE00003471775	30724370	30724451
ENSE00003478271	30716508	30716676
ENSE00003535329	30720811	30720915
ENSE00003573811	30714959	30715141
ENSE00003598868	30728648	30729325
ENSE00003601505	30719079	30719225
ENSE00003602469	30711566	30711629
ENSE00003638705	30725966	30726088
ENSE00003653467	30723259	30723314
ENSE00003665248	30730239	30730282
ENSE00003670565	30731343	30731510
ENSE00003688381	30751071	30751133
ENSE00003689607	30713785	30713885
ENSE00003961177	30709553	30710470
ENSE00003963637	30754751	30754951

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 97.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.8481 / max 324.2823, expressed in 1701 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
130327	4.2466	1319
130324	2.7791	1283
130325	1.0815	657
130326	0.2968	127
130321	0.1602	50
130322	0.1519	50
130320	0.1320	47

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
dorsal root ganglion	UBERON:0000044	97.23	gold quality
cerebellar vermis	UBERON:0004720	97.01	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.89	gold quality
cerebellar cortex	UBERON:0002129	96.66	gold quality
cerebellar hemisphere	UBERON:0002245	96.65	gold quality
cerebellum	UBERON:0002037	96.43	gold quality
trigeminal ganglion	UBERON:0001675	96.18	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	95.75	gold quality
sural nerve	UBERON:0015488	95.57	gold quality
lateral nuclear group of thalamus	UBERON:0002736	95.49	gold quality
substantia nigra pars compacta	UBERON:0001965	95.20	gold quality
substantia nigra pars reticulata	UBERON:0001966	94.38	gold quality
lateral globus pallidus	UBERON:0002476	93.97	gold quality
secondary oocyte	CL:0000655	93.92	gold quality
right frontal lobe	UBERON:0002810	93.83	gold quality
postcentral gyrus	UBERON:0002581	93.76	gold quality
superior frontal gyrus	UBERON:0002661	93.47	gold quality
middle temporal gyrus	UBERON:0002771	93.40	gold quality
parietal lobe	UBERON:0001872	93.24	gold quality
primary visual cortex	UBERON:0002436	93.03	gold quality
CA1 field of hippocampus	UBERON:0003881	92.89	gold quality
superior vestibular nucleus	UBERON:0007227	92.89	gold quality
peripheral nervous system	UBERON:0000010	92.86	gold quality
nerve	UBERON:0001021	92.86	gold quality
tibial nerve	UBERON:0001323	92.86	gold quality
pituitary gland	UBERON:0000007	92.83	gold quality
pons	UBERON:0000988	92.70	gold quality
nucleus accumbens	UBERON:0001882	92.62	gold quality
Brodmann (1909) area 46	UBERON:0006483	92.43	gold quality
orbitofrontal cortex	UBERON:0004167	92.32	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

74 targeting CAPRIN2, 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-4533	100.00	69.48	2758
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
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

Literature-anchored findings (GeneRIF, showing 7)

• regulated expression of EEG-1 is involved in the orchestrated regulation of growth that occurs as erythroblasts shift from a highly proliferative state toward their terminal phase of differentiation. (PMID:14593112)
• Caprin-2 promotes activation of the canonical Wnt signaling pathway by regulating LRP5/6 phosphorylation. (PMID:18762581)
• Caprin-2 C1q-related domain forms a flexible homotrimer mediated by calcium, and this trimeric assembly is required for the functioning of caprin-2. (PMID:25331957)
• findings revealed an unrecognized role of Caprin-2 in facilitating LRP5/6 constitutive phosphorylation at G2/M through forming a quaternary complex with CDK14, Cyclin Y, and LRP5/6. (PMID:27821587)
• LINC00941 promotes oral squamous cell carcinoma progression via activating CAPRIN2 and canonical WNT/beta-catenin signaling pathway. (PMID:32691935)
• Upregulated lncRNA Cyclin-dependent kinase inhibitor 2B antisense RNA 1 induces the proliferation and migration of colorectal cancer by miR-378b/CAPRIN2 axis. (PMID:34511033)
• Polymorphisms in TRIB2 and CAPRIN2 Genes Contribute to the Susceptibility to High Myopia-Induced Cataract in Han Chinese Population. (PMID:36710479)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	caprin2	ENSDARG00000020749
mus_musculus	Caprin2	ENSMUSG00000030309
rattus_norvegicus	Caprin2	ENSRNOG00000047319
drosophila_melanogaster	Capr	FBGN0042134

Paralogs (1): CAPRIN1 (ENSG00000135387)

Protein

Protein identifiers

Caprin-2 — Q6IMN6 (reviewed: Q6IMN6)

Alternative names: C1q domain-containing protein 1, Cytoplasmic activation/proliferation-associated protein 2, Gastric cancer multidrug resistance-associated protein, Protein EEG-1, RNA granule protein 140

All UniProt accessions (25): Q6IMN6, A0A8I5KPA6, A0A8I5KRN0, A0A8I5KSM9, A0A8I5KUX4, A0A8I5KUY8, A0A8I5KZC0, A0A8Q3SHE9, A0A8Q3SHP6, A0A8Q3SHS5, A0A8Q3SHV1, A0A8Q3SHW1, A0A8Q3WKC4, A0A8Q3WKE6, A0A8Q3WKE7, A0A8Q3WKF3, A0A8Q3WLH0, F5GXI7, F5GYA1, F5GZX3, F5H142, F5H5J8, H0YGG3, H0YID4, H3BM22

UniProt curated annotations — full annotation on UniProt →

Function. Promotes phosphorylation of the Wnt coreceptor LRP6, leading to increased activity of the canonical Wnt signaling pathway. Facilitates constitutive LRP6 phosphorylation by CDK14/CCNY during G2/M stage of the cell cycle, which may potentiate cells for Wnt signaling. May regulate the transport and translation of mRNAs, modulating for instance the expression of proteins involved in synaptic plasticity in neurons. Involved in regulation of growth as erythroblasts shift from a highly proliferative state towards their terminal phase of differentiation. May be involved in apoptosis.

Subunit / interactions. Homotrimer; via C1q domain. Found in a complex with LRP6, CCNY and CDK14 during G2/M stage; CAPRIN2 functions as a scaffold for the complex by binding to CCNY via its N terminus and to CDK14 via its C terminus. Interacts with LRP5. Interacts with LRP6.

Subcellular location. Cytoplasm Mitochondrion. Cytoplasm Mitochondrion Cell membrane.

Tissue specificity. Detected in all tissues tested with highest levels of expression in brain and spleen.

Domain organisation. The C1q domain is essential for the function in Wnt signaling.

Similarity. Belongs to the caprin family.

Isoforms (9)

UniProt ID	Names	Canonical?
Q6IMN6-1	1	yes
Q6IMN6-2	2, EEG-1L
Q6IMN6-3	3
Q6IMN6-4	4
Q6IMN6-5	5, EEG-1S
Q6IMN6-6	6
Q6IMN6-7	7
Q6IMN6-9	9
Q6IMN6-10	10

RefSeq proteins (66): NP_001002259, NP_001193785, NP_001306771, NP_001306772, NP_001306773, NP_001306774, NP_001306775, NP_001372427, NP_001372428, NP_001372429, NP_001372430, NP_001372431, NP_001372432, NP_001372433, NP_001372434, NP_001372435, NP_001372436, NP_001372437, NP_001372438, NP_001372439, NP_001372440, NP_001372441, NP_001372442, NP_001372443, NP_001372444, NP_001372445, NP_001372447, NP_001372448, NP_001372449, NP_001372450, NP_001372451, NP_001372452, NP_001372453, NP_001372454, NP_001372455, NP_001372456, NP_001372457, NP_001372458, NP_001372460, NP_001372461, NP_001372462, NP_001372463, NP_001372464, NP_001372466, NP_001372467, NP_001372468, NP_001372469, NP_001372470, NP_001372471, NP_001372472, NP_001372473, NP_001372474, NP_001372475, NP_001372476, NP_001372477, NP_001372478, NP_001372479, NP_001372480, NP_001372481, NP_001372482, NP_001372483, NP_001372486, NP_001372488, NP_001403442, NP_076414, NP_115532 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001073	C1q_dom	Domain
IPR008983	Tumour_necrosis_fac-like_dom	Homologous_superfamily
IPR022070	Caprin-1_C	Domain
IPR028816	Caprin	Family
IPR041637	Caprin-1_dimer	Domain

Pfam: PF00386, PF12287, PF18293

UniProt features (68 total): strand 13, splice variant 11, compositionally biased region 9, helix 9, mutagenesis site 6, region of interest 4, sequence variant 4, sequence conflict 3, binding site 2, modified residue 2, coiled-coil region 2, chain 1, domain 1, turn 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
4OUM	X-RAY DIFFRACTION	1.49
4OUL	X-RAY DIFFRACTION	1.95
8K9C	X-RAY DIFFRACTION	2.32
5J97	X-RAY DIFFRACTION	2.55
8K9D	X-RAY DIFFRACTION	3.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6IMN6-F1	52.42	0.22

Functional residue map

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

Ligand- & substrate-binding residues (2): 1078; 1084

Post-translational modifications (2): 948, 949

Mutagenesis-validated functional residues (6):

Position	Phenotype
1048	impaired homotrimer formation. no effect on lrp6 binding although lrp6 phosphorylation is significantly reduced.
1078	loss of calcium binding and increased homotrimer stability; when associated with ala-1084.
1084	loss of calcium binding and increased homotrimer stability; when associated with ala-1078.
1091	impaired homotrimer formation. no effect on lrp6 binding although lrp6 phosphorylation is significantly reduced.
1114	no effect on homotrimer formation.
1122	no effect on homotrimer formation.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 239 (showing top): GOBP_DENDRITE_DEVELOPMENT, MULLIGHAN_NPM1_SIGNATURE_3_UP, GOBP_AXIS_SPECIFICATION, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_NEGATIVE_REGULATION_OF_CELL_GROWTH, GOBP_REGULATION_OF_DENDRITE_MORPHOGENESIS, GOBP_DENDRITIC_SPINE_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_GROWTH, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_DORSAL_VENTRAL_PATTERN_FORMATION, GOBP_NEGATIVE_REGULATION_OF_TRANSLATION

GO Biological Process (8): dorsal/ventral axis specification (GO:0009950), negative regulation of translation (GO:0017148), cell differentiation (GO:0030154), negative regulation of cell growth (GO:0030308), positive regulation of transcription by RNA polymerase II (GO:0045944), positive regulation of dendrite morphogenesis (GO:0050775), positive regulation of dendritic spine morphogenesis (GO:0061003), positive regulation of canonical Wnt signaling pathway (GO:0090263)

GO Molecular Function (4): RNA binding (GO:0003723), signaling receptor binding (GO:0005102), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (8): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), mitochondrion (GO:0005739), centrosome (GO:0005813), cytosol (GO:0005829), plasma membrane (GO:0005886), signaling receptor complex (GO:0043235), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
cytoplasm	2
axis specification	1
dorsal/ventral pattern formation	1
translation	1
regulation of translation	1
negative regulation of gene expression	1
negative regulation of protein metabolic process	1
cellular developmental process	1
regulation of cell growth	1
cell growth	1
negative regulation of growth	1
negative regulation of cellular process	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
positive regulation of cell morphogenesis	1
positive regulation of cell projection organization	1
dendrite morphogenesis	1
regulation of dendrite morphogenesis	1
positive regulation of neurogenesis	1
positive regulation of neuron projection development	1
positive regulation of dendrite morphogenesis	1
dendritic spine morphogenesis	1
positive regulation of dendritic spine development	1
regulation of dendritic spine morphogenesis	1
positive regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
regulation of canonical Wnt signaling pathway	1
nucleic acid binding	1
protein binding	1
cation binding	1
binding	1
nuclear lumen	1
intracellular anatomical structure	1
intracellular membrane-bounded organelle	1
centriole	1
microtubule organizing center	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

394 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CAPRIN2	LRP5	O75197	754
CAPRIN2	TDRD7	Q8NHU6	581
CAPRIN2	CCNY	Q8ND76	548
CAPRIN2	C1QTNF12	Q5T7M4	455
CAPRIN2	PURA	Q00577	434
CAPRIN2	TRPC4AP	Q8TEL6	397
CAPRIN2	OR5I1	Q13606	397
CAPRIN2	CRYGS	P22914	396
CAPRIN2	DNASE2B	Q8WZ79	392
CAPRIN2	RNF169	Q8NCN4	391
CAPRIN2	VPS52	Q8N1B4	390
CAPRIN2	YBX1	P16990	380
CAPRIN2	KLHL22	Q53GT1	370
CAPRIN2	CDK14	O94921	368
CAPRIN2	DAZAP2	Q15038	368

IntAct

13 interactions, top by confidence:

A	B	Type	Score
AUP1	UBE2G2	psi-mi:“MI:0914”(association)	0.750
PEX5	CAPRIN2	psi-mi:“MI:0915”(physical association)	0.560
LRP5	CAPRIN2	psi-mi:“MI:0915”(physical association)	0.520
CAPRIN2	LRP5	psi-mi:“MI:0915”(physical association)	0.520
CAPRIN2	NPM1	psi-mi:“MI:0915”(physical association)	0.400
LRP6	CAPRIN2	psi-mi:“MI:0915”(physical association)	0.400
COPS6	DDX3X	psi-mi:“MI:0914”(association)	0.350
FAM8A1	OS9	psi-mi:“MI:0914”(association)	0.350
FERMT2	CAPRIN2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): CAPRIN2 (Two-hybrid), CAPRIN2 (Affinity Capture-MS), CAPRIN2 (Affinity Capture-MS), CAPRIN2 (Affinity Capture-MS), CAPRIN2 (Two-hybrid), CAPRIN2 (Proximity Label-MS), CAPRIN2 (Proximity Label-MS), CAPRIN2 (Proximity Label-MS), CAPRIN2 (Affinity Capture-MS), CAPRIN2 (Cross-Linking-MS (XL-MS)), CAPRIN2 (Cross-Linking-MS (XL-MS)), CAPRIN2 (Protein-RNA), CAPRIN2 (Affinity Capture-MS), CAPRIN2 (Affinity Capture-Western), LRP6 (Affinity Capture-Western)

ESM2 similar proteins: A0A1B0GVQ3, A0A1W2PPK0, A0A1W2PPM1, A2A9I7, A6NCI8, A6QQS3, A7XCE8, E9PI22, E9PXT9, O15016, O91083, P09414, P0DMB1, P17923, P18804, P20879, P35965, P49750, Q0P670, Q12857, Q1RMX6, Q32LN6, Q32MG2, Q3B8N5, Q3T016, Q3V0A6, Q4JK59, Q5BI31, Q5T035, Q5ZKH6, Q642A3, Q6AXV6, Q6IMN6, Q6P1W5, Q6PEX7, Q6X4T0, Q80YD3, Q86UF4, Q8BII1, Q8C5V0

Diamond homologs: A0A060WQA3, A5PN28, A6NHN0, B2RNN3, O75973, O88992, P02745, P02746, P08125, P0C862, P14106, P14282, P23206, P25067, P25318, P27658, P31720, P31721, P83371, P98085, P98086, Q00780, Q02105, Q03692, Q05306, Q05A80, Q06575, Q06576, Q06577, Q0II24, Q15848, Q2KIU3, Q2KIX7, Q3Y5Z3, Q4ZJM7, Q4ZJM9, Q4ZJN1, Q5E9E3, Q5FVH0, Q5RJ80

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
CAPRIN2	up-regulates	LRP6	binding
CAPRIN2	“up-regulates quantity by stabilization”	OXT	“post transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	135
Likely benign	6
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

3531 predictions. Top by Δscore:

Variant	Effect	Δscore
12:30710544:CTA:C	acceptor_gain	1.0000
12:30710545:TA:T	acceptor_gain	1.0000
12:30710547:C:CC	acceptor_gain	1.0000
12:30713779:ACTT:A	donor_loss	1.0000
12:30713781:TTA:T	donor_loss	1.0000
12:30713782:TA:T	donor_loss	1.0000
12:30713783:A:AC	donor_gain	1.0000
12:30713783:AC:A	donor_gain	1.0000
12:30713784:C:CC	donor_gain	1.0000
12:30713784:CC:C	donor_gain	1.0000
12:30713784:CCCT:C	donor_gain	1.0000
12:30713883:AACC:A	acceptor_loss	1.0000
12:30713884:ACC:A	acceptor_loss	1.0000
12:30713887:T:G	acceptor_loss	1.0000
12:30716507:CCAGT:C	donor_gain	1.0000
12:30719077:A:AC	donor_gain	1.0000
12:30719078:C:CC	donor_gain	1.0000
12:30719078:CTGT:C	donor_gain	1.0000
12:30720805:TTTTA:T	donor_loss	1.0000
12:30720806:TTTAC:T	donor_loss	1.0000
12:30720807:TTACC:T	donor_loss	1.0000
12:30720808:TA:T	donor_loss	1.0000
12:30720809:ACCTC:A	donor_loss	1.0000
12:30720810:C:CT	donor_loss	1.0000
12:30720911:GTAGC:G	acceptor_gain	1.0000
12:30720912:TAGC:T	acceptor_gain	1.0000
12:30720914:GCC:G	acceptor_loss	1.0000
12:30720916:C:CC	acceptor_gain	1.0000
12:30720916:CT:C	acceptor_loss	1.0000
12:30723254:GTTA:G	donor_loss	1.0000

AlphaMissense

6842 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000032084 (12:30722620 G>C), RS1000054884 (12:30746092 T>C,G), RS1000119305 (12:30752974 G>A), RS1000222894 (12:30732918 T>C,G), RS1000269264 (12:30739912 T>C), RS1000313679 (12:30752394 C>G), RS1000425871 (12:30748432 T>C), RS1000460487 (12:30742014 A>G), RS1000518957 (12:30748144 G>C), RS1000563719 (12:30711463 A>G), RS1000583436 (12:30734548 C>A,T), RS1000726291 (12:30754508 C>A), RS1000831296 (12:30727024 C>G), RS1000918482 (12:30721941 AGAGC>A), RS1000990799 (12:30754702 G>C)

Disease associations

OMIM: gene MIM:610375 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST008363_89	Offspring birth weight	3.000000e-14
GCST008839_74	Height	3.000000e-08
GCST009391_318	Metabolite levels	2.000000e-06
GCST012013_26	Cataracts	4.000000e-09
GCST013216_3	Order dimension in obsessive compulsive disorder	4.000000e-06
GCST90014268_26	Cataracts	3.000000e-22
GCST90020024_264	A body shape index	5.000000e-08

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004344	birth weight
EFO:0005939	parental genotype effect measurement
EFO:0010431	triacylglycerol 56:4 measurement
EFO:0007802	obsessive-compulsive symptom measurement
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	increases expression	3
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
sodium arsenite	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
alpha phellandrene	increases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
titanium dioxide	decreases methylation	1
beta-lapachone	increases expression	1
cobaltous chloride	increases expression	1
16 alpha-ethyl-21-hydroxy-19-nor-4-pregnene-3,20-dione	increases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
nickel sulfate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects cotreatment, decreases expression, affects response to substance	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
(+)-JQ1 compound	increases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Air Pollutants, Occupational	affects expression	1
Arsenic	decreases expression, increases abundance	1
Dexamethasone	affects cotreatment, decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1

Clinical trials (associated diseases)

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