CAMSAP1

Summary

CAMSAP1 (calmodulin regulated spectrin associated protein 1, HGNC:19946) is a protein-coding gene on chromosome 9q34.3, encoding Calmodulin-regulated spectrin-associated protein 1 (Q5T5Y3). Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization.

Enables microtubule minus-end binding activity and spectrin binding activity. Involved in several processes, including neuron projection development; regulation of cell morphogenesis; and regulation of microtubule polymerization. Located in microtubule minus-end. Implicated in complex cortical dysplasia with other brain malformations.

Source: NCBI Gene 157922 — RefSeq curated summary.

At a glance

• Gene–disease (curated): cortical dysplasia, complex, with other brain malformations 12 (Strong, GenCC)
• Clinical variants (ClinVar): 299 total — 1 pathogenic, 4 likely-pathogenic
• Phenotypes (HPO): 29
• MANE Select transcript: NM_015447

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19946
Approved symbol	CAMSAP1
Name	calmodulin regulated spectrin associated protein 1
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31228, DKFZp434F195
Ensembl gene	ENSG00000130559
Ensembl biotype	protein_coding
OMIM	613774
Entrez	157922

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding_CDS_not_defined, 3 protein_coding, 2 retained_intron

ENST00000312405, ENST00000389532, ENST00000409386, ENST00000460094, ENST00000468150, ENST00000482664, ENST00000483991, ENST00000487868, ENST00000492174, ENST00000493088

RefSeq mRNA: 2 — MANE Select: NM_015447 NM_001411031, NM_015447

CCDS: CCDS35176, CCDS94531

Canonical transcript exons

ENST00000389532 — 17 exons

Exon	Start	End
ENSE00001601940	135882816	135883078
ENSE00001680093	135827407	135827584
ENSE00001703747	135907000	135907546
ENSE00001723846	135862467	135862608
ENSE00001790032	135850137	135850233
ENSE00001820635	135808487	135811611
ENSE00003480671	135815890	135816005
ENSE00003510489	135850322	135850461
ENSE00003558953	135823950	135824034
ENSE00003564095	135817977	135818079
ENSE00003618482	135881633	135881794
ENSE00003619962	135815097	135815215
ENSE00003627212	135820839	135823260
ENSE00003631522	135866456	135866536
ENSE00003644614	135824789	135824880
ENSE00003644680	135819010	135819146
ENSE00003692607	135818408	135818616

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 97.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.4309 / max 157.0507, expressed in 1803 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
103106	9.2163	1742
103107	8.2147	1754

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	97.25	gold quality
buccal mucosa cell	CL:0002336	95.81	gold quality
endothelial cell	CL:0000115	95.76	gold quality
oocyte	CL:0000023	95.60	gold quality
cortical plate	UBERON:0005343	95.24	gold quality
ganglionic eminence	UBERON:0004023	94.17	gold quality
sperm	CL:0000019	94.12	gold quality
ventricular zone	UBERON:0003053	93.92	gold quality
middle temporal gyrus	UBERON:0002771	93.74	gold quality
male germ cell	CL:0000015	92.46	gold quality
amniotic fluid	UBERON:0000173	92.45	gold quality
cervix squamous epithelium	UBERON:0006922	92.35	silver quality
Brodmann (1909) area 23	UBERON:0013554	91.92	gold quality
tongue squamous epithelium	UBERON:0006919	91.83	gold quality
squamous epithelium	UBERON:0006914	91.33	gold quality
gastrocnemius	UBERON:0001388	91.26	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.23	gold quality
embryo	UBERON:0000922	90.97	gold quality
gingival epithelium	UBERON:0001949	90.93	gold quality
esophagus squamous epithelium	UBERON:0006920	90.91	gold quality
epithelium of esophagus	UBERON:0001976	90.89	gold quality
muscle of leg	UBERON:0001383	90.84	gold quality
gingiva	UBERON:0001828	89.62	gold quality
corpus callosum	UBERON:0002336	89.52	gold quality
cervix epithelium	UBERON:0004801	89.43	gold quality
endometrium epithelium	UBERON:0004811	89.41	gold quality
cerebellum	UBERON:0002037	89.01	gold quality
cerebellar cortex	UBERON:0002129	88.98	gold quality
cerebellar hemisphere	UBERON:0002245	88.96	gold quality
right hemisphere of cerebellum	UBERON:0014890	88.95	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-137537	no	3.26
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

143 targeting CAMSAP1, 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-3646	100.00	73.56	5283
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-95-5P	99.89	72.17	3973

Literature-anchored findings (GeneRIF, showing 6)

• The CKK domain binds microtubules and represents a domain that evolved with the metazoa. (PMID:19508979)
• Results show that Camsap1 is related with the prognosis of laryngeal squamous cell carcinoma patients. Its expression inducs microtubule formation and aggregation. (PMID:24603804)
• These results show that members of the CAMSAP/Patronin family all localize to and protect minus-ends but have evolved distinct effects on microtubule dynamics. (PMID:24706919)
• Calmodulin Regulated Spectrin Associated Protein 1 mRNA is Directly Regulated by miR-126 in Primary Human Osteoblasts (PMID:27958650)
• The CAMSAP1 CKK domain remodels its microtubule interaction site and changes the underlying polymer structure because the tubulin lattice conformation is not optimal for its binding. Thus, in contrast to many microtubule associated proteins, the human CKK domain can differentiate subtly specific tubulin conformations to enable microtubule minus-end recognition. (PMID:31748546)
• Bi-allelic CAMSAP1 variants cause a clinically recognizable neuronal migration disorder. (PMID:36283405)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	camsap1a	ENSDARG00000019208
danio_rerio	camsap1b	ENSDARG00000035122
mus_musculus	Camsap1	ENSMUSG00000026933
rattus_norvegicus	Camsap1	ENSRNOG00000017883
drosophila_melanogaster	Patronin	FBGN0263197
caenorhabditis_elegans		WBGENE00004121

Paralogs (2): CAMSAP3 (ENSG00000076826), CAMSAP2 (ENSG00000118200)

Protein

Protein identifiers

Calmodulin-regulated spectrin-associated protein 1 — Q5T5Y3 (reviewed: Q5T5Y3)

All UniProt accessions (2): Q5T5Y3, A0A384NY94

UniProt curated annotations — full annotation on UniProt →

Function. Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization. Specifically recognizes growing microtubule minus-ends and stabilizes microtubules. Acts on free microtubule minus-ends that are not capped by microtubule-nucleating proteins or other factors and protects microtubule minus-ends from depolymerization. In contrast to CAMSAP2 and CAMSAP3, tracks along the growing tips of minus-end microtubules without significantly affecting the polymerization rate: binds at the very tip of the microtubules minus-end and acts as a minus-end tracking protein (-TIP) that dissociates from microtubules after allowing tubulin incorporation. Through interaction with spectrin may regulate neurite outgrowth.

Subunit / interactions. Interacts with spectrin via SPTBN1; the interaction is direct. Interacts with calmodulin; calcium-dependent it prevents interaction with spectrin.

Subcellular location. Cytoplasm. Cytoskeleton.

Disease relevance. Cortical dysplasia, complex, with other brain malformations 12 (CDCBM12) [MIM:620316] An autosomal recessive disorder of aberrant neuronal migration during brain development. CDCBM12 is characterized by severe to profound neurodevelopmental delay, microcephaly, cortical visual impairment, craniofacial dysmorphism, and seizures. Brain imaging shows lissencephaly, severe hypoplasia or absence of the corpus callosum, cerebellar hypodysplasia, and dysplasia of the basal ganglia, hippocampus and midbrain. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The CKK domain binds microtubules.

Similarity. Belongs to the CAMSAP1 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5T5Y3-1	1	yes
Q5T5Y3-2	2
Q5T5Y3-3	3

RefSeq proteins (2): NP_001397960, NP_056262* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001715	CH_dom	Domain
IPR011033	PRC_barrel-like_sf	Homologous_superfamily
IPR014797	CKK_CAMSAP	Domain
IPR022613	CH_CAMSAP_2	Domain
IPR031372	CAMSAP_CC1	Conserved_site
IPR032940	CAMSAP	Family
IPR036872	CH_dom_sf	Homologous_superfamily
IPR038209	CKK_dom_sf	Homologous_superfamily
IPR058042	CAMSAP_N	Domain

Pfam: PF08683, PF11971, PF17095, PF25532

UniProt features (54 total): modified residue 18, compositionally biased region 12, region of interest 9, sequence variant 5, coiled-coil region 3, domain 2, splice variant 2, chain 1, mutagenesis site 1, sequence conflict 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
6QUS	ELECTRON MICROSCOPY	3.7
6QVJ	ELECTRON MICROSCOPY	3.8
5M5C	ELECTRON MICROSCOPY	4.8
5M54	ELECTRON MICROSCOPY	8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T5Y3-F1	55.21	0.20

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 (18): 217, 371, 375, 416, 431, 512, 563, 575, 589, 629, 722, 728, 738, 740, 1080, 1398, 1427, 1537

Mutagenesis-validated functional residues (1):

Position	Phenotype
885–888	loss of interaction with sptbn1.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 253 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, MITSIADES_RESPONSE_TO_APLIDIN_DN, GOBP_NEUROGENESIS, BROWNE_HCMV_INFECTION_16HR_UP, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_MICROTUBULE_POLYMERIZATION, TGCTGAY_UNKNOWN, TCF11_01, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, MORF_IKBKG, GOBP_CELL_PROJECTION_ORGANIZATION

GO Biological Process (5): microtubule cytoskeleton organization (GO:0000226), cytoskeleton organization (GO:0007010), regulation of cell morphogenesis (GO:0022604), regulation of microtubule polymerization (GO:0031113), neuron projection development (GO:0031175)

GO Molecular Function (5): calmodulin binding (GO:0005516), microtubule binding (GO:0008017), spectrin binding (GO:0030507), microtubule minus-end binding (GO:0051011), protein binding (GO:0005515)

GO Cellular Component (4): microtubule (GO:0005874), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), microtubule minus-end (GO:0036449)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoskeleton organization	1
microtubule-based process	1
organelle organization	1
cell morphogenesis	1
regulation of anatomical structure morphogenesis	1
regulation of microtubule polymerization or depolymerization	1
regulation of protein polymerization	1
microtubule polymerization	1
regulation of supramolecular fiber organization	1
neuron development	1
plasma membrane bounded cell projection organization	1
protein binding	1
tubulin binding	1
cytoskeletal protein binding	1
protein-containing complex binding	1
microtubule binding	1
binding	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1
microtubule end	1

Protein interactions and networks

STRING

976 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CAMSAP1	TUBG2	Q9NRH3	495
CAMSAP1	ZNF614	Q8N883	489
CAMSAP1	FAM120A	Q9NZB2	483
CAMSAP1	SPTBN1	Q01082	477
CAMSAP1	CLNS1A	P54105	476
CAMSAP1	FBXW4	P57775	476
CAMSAP1	SNAPC4	Q5SXM2	452
CAMSAP1	CCNYL1	Q8N7R7	449
CAMSAP1	CLRN3	Q8NCR9	448
CAMSAP1	SURF6	O75683	448
CAMSAP1	MSANTD2	Q6P1R3	448
CAMSAP1	ZKSCAN1	P17029	446
CAMSAP1	AK8	Q96MA6	443
CAMSAP1	ESYT2	A0FGR8	439
CAMSAP1	NUP54	Q7Z3B4	433

IntAct

68 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
CEP170	KIF2A	psi-mi:“MI:2364”(proximity)	0.650
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
MFHAS1	PGRMC2	psi-mi:“MI:0914”(association)	0.590
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
CEP104	CCDC66	psi-mi:“MI:2364”(proximity)	0.540
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
KIAA0753	OFD1	psi-mi:“MI:2364”(proximity)	0.480
MAP1LC3B	CAMSAP1	psi-mi:“MI:0407”(direct interaction)	0.440
MAP1LC3A	CAMSAP1	psi-mi:“MI:0407”(direct interaction)	0.440
SPTBN1	CAMSAP1	psi-mi:“MI:0407”(direct interaction)	0.440
CAMSAP1	HMGA1	psi-mi:“MI:0915”(physical association)	0.400
CALM1	CAMSAP1	psi-mi:“MI:0915”(physical association)	0.400
CAMSAP1	SKIL	psi-mi:“MI:0915”(physical association)	0.370
CAMSAP1	SMAD1	psi-mi:“MI:0915”(physical association)	0.370
CAMSAP1	SMAD9	psi-mi:“MI:0915”(physical association)	0.370
RBPJ	SAMD1	psi-mi:“MI:0914”(association)	0.350
EGLN3	FAM168B	psi-mi:“MI:0914”(association)	0.350
Mecom	ESYT2	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
	CCDC22	psi-mi:“MI:0914”(association)	0.350
DYRK1A	TEX13D	psi-mi:“MI:0914”(association)	0.350
TUBB4B	TUBA1B	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
MRFAP1L1	MYO9A	psi-mi:“MI:0914”(association)	0.350
KIF3A	UBA6	psi-mi:“MI:0914”(association)	0.350
PCM1	CCDC66	psi-mi:“MI:2364”(proximity)	0.270
CEP128	CCDC66	psi-mi:“MI:2364”(proximity)	0.270
LCA5	DVL2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (118): CAMSAP1 (Affinity Capture-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Biochemical Activity), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS), CAMSAP1 (Proximity Label-MS)

ESM2 similar proteins: A0A1L8EYB2, A0JMF7, A2AHC3, A3KMW7, A5D8S0, A5WUN7, B0S6S9, D3Z8E6, D3Z987, F1M5M3, F1MJR8, F1QB81, P70347, P97412, Q0P5X5, Q0VET5, Q15468, Q2M2Z5, Q2T9I9, Q3UEN2, Q3V0M2, Q49A88, Q49AJ0, Q5CZC0, Q5RA75, Q5RHB5, Q5SW75, Q5T5Y3, Q60664, Q6JPI3, Q6NRK3, Q6PUR7, Q71F56, Q76I76, Q7M6U3, Q7TSH4, Q8C753, Q8CCC3, Q8IWB6, Q8K2J4

Diamond homologs: A1ZAU8, A2AHC3, A5WUN7, D3Z8E6, D4AEC2, Q08AD1, Q5T5Y3, Q6IRN6, Q80VC9, Q8C1B1, Q9P1Y5, U4PAZ9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 84 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Activation of BAD and translocation to mitochondria	7	96.9×	4e-11
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	85.5×	7e-11
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	85.5×	7e-11
Activation of BH3-only proteins	7	63.2×	3e-10
RHO GTPases activate PKNs	7	40.4×	9e-09
Intrinsic Pathway for Apoptosis	7	37.3×	1e-08
Translocation of SLC2A4 (GLUT4) to the plasma membrane	11	30.9×	2e-11
FOXO-mediated transcription	5	30.5×	7e-06

GO biological processes:

GO term	Partners	Fold	FDR
protein targeting	5	25.4×	1e-04
intracellular protein localization	10	14.5×	4e-07
cilium assembly	9	9.2×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	4
Uncertain significance	231
Likely benign	30
Benign	4

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
1527564	GRCh37/hg19 9q34.3(chr9:138740078-141020389)	Pathogenic
1706468	NM_015447.4(CAMSAP1):c.1831A>T (p.Lys611Ter)	Likely pathogenic
4845349	NM_015447.4(CAMSAP1):c.3919C>T (p.Gln1307Ter)	Likely pathogenic
972931	NM_015447.4(CAMSAP1):c.1707dup (p.Thr570fs)	Likely pathogenic
972932	NM_015447.4(CAMSAP1):c.3130C>T (p.Gln1044Ter)	Likely pathogenic

SpliceAI

3966 predictions. Top by Δscore:

Variant	Effect	Δscore
9:135811611:CCTG:C	acceptor_gain	1.0000
9:135815093:TTGCC:T	donor_loss	1.0000
9:135815094:TGCCT:T	donor_loss	1.0000
9:135815217:T:G	acceptor_loss	1.0000
9:135815898:TCGGC:T	donor_gain	1.0000
9:135815899:CGGCC:C	donor_gain	1.0000
9:135816004:CT:C	acceptor_gain	1.0000
9:135817976:CCG:C	donor_gain	1.0000
9:135818084:C:CT	acceptor_gain	1.0000
9:135818084:C:T	acceptor_gain	1.0000
9:135818406:A:AC	donor_gain	1.0000
9:135818407:C:CC	donor_gain	1.0000
9:135818407:CGG:C	donor_gain	1.0000
9:135819006:TTA:T	donor_loss	1.0000
9:135819007:TACCG:T	donor_loss	1.0000
9:135819008:A:AC	donor_gain	1.0000
9:135819008:A:C	donor_loss	1.0000
9:135819009:C:CC	donor_gain	1.0000
9:135819009:C:CT	donor_loss	1.0000
9:135819009:CCGG:C	donor_gain	1.0000
9:135819009:CCGGG:C	donor_gain	1.0000
9:135819142:TCATC:T	acceptor_gain	1.0000
9:135819143:CATC:C	acceptor_gain	1.0000
9:135819143:CATCC:C	acceptor_gain	1.0000
9:135819144:ATC:A	acceptor_gain	1.0000
9:135819145:TC:T	acceptor_gain	1.0000
9:135819145:TCC:T	acceptor_loss	1.0000
9:135819146:CC:C	acceptor_gain	1.0000
9:135819147:C:CC	acceptor_gain	1.0000
9:135819147:CTG:C	acceptor_loss	1.0000

AlphaMissense

10579 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:135811382:G:T	A1579E	1.000
9:135811383:C:G	A1579P	1.000
9:135811424:A:G	F1565S	1.000
9:135811490:C:T	G1543E	1.000
9:135811574:A:G	L1515P	1.000
9:135811577:A:T	I1514K	1.000
9:135811357:C:A	W1587C	0.999
9:135811357:C:G	W1587C	0.999
9:135811359:A:G	W1587R	0.999
9:135811359:A:T	W1587R	0.999
9:135811373:A:T	I1582N	0.999
9:135811379:A:G	L1580P	0.999
9:135811386:C:G	D1578H	0.999
9:135811390:A:C	S1576R	0.999
9:135811390:A:T	S1576R	0.999
9:135811392:T:G	S1576R	0.999
9:135811423:A:C	F1565L	0.999
9:135811423:A:T	F1565L	0.999
9:135811425:A:G	F1565L	0.999
9:135811430:T:A	K1563I	0.999
9:135811446:A:C	Y1558D	0.999
9:135811446:A:G	Y1558H	0.999
9:135811449:T:C	K1557E	0.999
9:135811452:A:C	Y1556D	0.999
9:135811491:C:A	G1543W	0.999
9:135811491:C:G	G1543R	0.999
9:135811491:C:T	G1543R	0.999
9:135811496:C:T	G1541D	0.999
9:135811497:C:G	G1541R	0.999
9:135811539:A:C	Y1527D	0.999

dbSNP variants (sampled 300 via entrez): RS1000007141 (9:135871167 G>A), RS1000011564 (9:135846673 C>A,T), RS1000022899 (9:135909061 T>A), RS1000044527 (9:135864924 G>A), RS1000056506 (9:135870550 T>C,G), RS1000081501 (9:135891641 C>T), RS1000128880 (9:135819616 CTGAGGTCAGGAGTTCA>C), RS1000143899 (9:135820011 G>A), RS1000181532 (9:135812656 G>A,T), RS1000191004 (9:135820085 G>A,C), RS1000221294 (9:135891514 A>G), RS1000268842 (9:135891798 G>T), RS1000279784 (9:135817400 T>G), RS1000289595 (9:135849436 C>T), RS1000331170 (9:135854408 C>T)

Disease associations

OMIM: gene MIM:613774 | disease phenotypes: MIM:620316

GenCC curated gene-disease

Disease	Classification	Inheritance
cortical dysplasia, complex, with other brain malformations 12	Strong	Autosomal recessive

Mondo (1): cortical dysplasia, complex, with other brain malformations 12 (MONDO:0957217)

Orphanet (0):

HPO phenotypes

29 total (29 of 29 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000028	Cryptorchidism
HP:0000218	High palate
HP:0000431	Wide nasal bridge
HP:0000483	Astigmatism
HP:0000540	Hypermetropia
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001274	Agenesis of corpus callosum
HP:0001302	Pachygyria
HP:0001321	Cerebellar hypoplasia
HP:0001339	Lissencephaly
HP:0001347	Hyperreflexia
HP:0002263	Exaggerated cupid’s bow
HP:0002509	Limb hypertonia
HP:0002521	Hypsarrhythmia
HP:0002650	Scoliosis
HP:0003487	Babinski sign
HP:0003593	Infantile onset
HP:0003819	Death in childhood
HP:0005445	Enlarged posterior fossa
HP:0005487	Prominent metopic ridge
HP:0010851	EEG with burst suppression
HP:0011968	Feeding difficulties
HP:0025102	Dysgenesis of the basal ganglia
HP:0030084	Clinodactyly
HP:0100541	Femoral hernia
HP:0100704	Cerebral visual impairment

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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	6
Arsenic	increases abundance, increases expression, decreases expression, affects methylation, affects cotreatment	3
Estradiol	increases expression, affects expression	3
sodium arsenite	affects cotreatment, increases abundance, increases expression, decreases expression	2
cobaltous chloride	increases expression	2
Benzo(a)pyrene	increases mutagenesis, decreases expression	2
Cyclosporine	increases expression	2
Aflatoxin B1	increases methylation	2
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
arsenite	increases methylation	1
butyraldehyde	decreases expression	1
manganese chloride	increases expression, affects cotreatment, increases abundance	1
coumarin	affects phosphorylation	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	decreases expression	1
beta-methylcholine	affects expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	decreases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	increases expression	1
Acrolein	increases abundance, affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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