CIMAP1D

Summary

CIMAP1D (CIMAP1 family member D, HGNC:26841) is a protein-coding gene on chromosome 19p13.3, encoding Protein CIMAP1D (Q3SX64).

Located in cytoplasmic microtubule.

Source: NCBI Gene 284451 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 81 total
• MANE Select transcript: NM_182577

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26841
Approved symbol	CIMAP1D
Name	CIMAP1 family member D
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40059
Ensembl gene	ENSG00000181781
Ensembl biotype	protein_coding
Entrez	284451

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000315489, ENST00000382696, ENST00000591681

RefSeq mRNA: 3 — MANE Select: NM_182577 NM_001385597, NM_001385600, NM_182577

CCDS: CCDS12027, CCDS92474

Canonical transcript exons

ENST00000315489 — 4 exons

Exon	Start	End
ENSE00001215495	472394	472501
ENSE00001215510	474621	474983
ENSE00003472619	467649	467762
ENSE00003915318	463361	464364

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 91.61.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0569 / max 39.0836, expressed in 6 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177898	0.0569	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	91.61	gold quality
left testis	UBERON:0004533	91.45	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.98	gold quality
testis	UBERON:0000473	87.18	gold quality
pancreatic ductal cell	CL:0002079	85.51	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.71	gold quality
left ventricle myocardium	UBERON:0006566	81.63	gold quality
cardiac muscle of right atrium	UBERON:0003379	81.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.77	gold quality
gastrocnemius	UBERON:0001388	78.19	gold quality
muscle of leg	UBERON:0001383	76.96	gold quality
quadriceps femoris	UBERON:0001377	74.97	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	74.84	gold quality
vastus lateralis	UBERON:0001379	74.61	gold quality
myocardium	UBERON:0002349	74.40	gold quality
sperm	CL:0000019	73.83	gold quality
skeletal muscle tissue	UBERON:0001134	72.78	gold quality
ileal mucosa	UBERON:0000331	71.67	silver quality
biceps brachii	UBERON:0001507	71.36	gold quality
nasal cavity epithelium	UBERON:0005384	70.86	gold quality
muscle tissue	UBERON:0002385	70.49	gold quality
upper arm skin	UBERON:0004263	68.46	gold quality
deltoid	UBERON:0001476	68.25	gold quality
heart right ventricle	UBERON:0002080	67.66	gold quality
superficial temporal artery	UBERON:0001614	67.41	gold quality
kidney epithelium	UBERON:0004819	65.22	gold quality
parotid gland	UBERON:0001831	64.94	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	64.09	gold quality
tibialis anterior	UBERON:0001385	63.51	silver quality
endothelial cell	CL:0000115	61.85	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting CIMAP1D, 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-4673	100.00	66.64	1490
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-3154	98.94	66.55	1455
HSA-MIR-1183	98.75	67.10	1116
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-6730-5P	98.03	68.12	1299
HSA-MIR-3661	97.83	67.30	705
HSA-MIR-6849-3P	97.25	64.57	1371
HSA-MIR-631	97.05	66.93	602
HSA-MIR-3918	96.13	64.65	1300
HSA-MIR-3943	95.87	64.57	523
HSA-MIR-6781-5P	94.61	59.49	155

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	odf3l2a	ENSDARG00000014209
danio_rerio	cimap1d	ENSDARG00000021432
mus_musculus	Cimap1d	ENSMUSG00000035963
rattus_norvegicus	Cimap1d	ENSRNOG00000008199

Paralogs (5): STPG1 (ENSG00000001460), STPG2 (ENSG00000163116), CIMAP1A (ENSG00000177947), CIMAP1B (ENSG00000177989), CIMAP1C (ENSG00000182950)

Protein

Protein identifiers

Protein CIMAP1D — Q3SX64 (reviewed: Q3SX64)

Alternative names: CIMAP1 family member D, Outer dense fiber protein 3-like protein 2

All UniProt accessions (1): Q3SX64

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CIMAP family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q3SX64-1	1	yes
Q3SX64-2	2

RefSeq proteins (3): NP_001372526, NP_001372529, NP_872383* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010736	SHIPPO-rpt	Repeat
IPR051291	CIMAP	Family

Pfam: PF07004

UniProt features (10 total): repeat 3, region of interest 3, chain 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3SX64-F1	67.70	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GOCC_CYTOPLASMIC_MICROTUBULE, chr19p13, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_DN, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_UP, GOCC_SUPRAMOLECULAR_POLYMER, GSE10147_IL3_AND_HIVP17_VS_IL3_AND_CPG_STIM_PDC_UP, GSE7568_CTRL_VS_3H_TGFB_TREATED_MACROPHAGES_WITH_IL4_AND_DEXAMETHASONE_UP, DESCARTES_MAIN_FETAL_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_ADRENAL_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_CEREBELLUM_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_CEREBRUM_VASCULAR_ENDOTHELIAL_CELLS, DESCARTES_FETAL_KIDNEY_VASCULAR_ENDOTHELIAL_CELLS

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): cytoskeleton (GO:0005856), cytoplasmic microtubule (GO:0005881)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membraneless organelle	1
cytoplasm	1
microtubule	1

Protein interactions and networks

STRING

438 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMAP1D	KLHL26	Q53HC5	591
CIMAP1D	SMIM7	Q9BQ49	582
CIMAP1D	ERICH3	Q5RHP9	541
CIMAP1D	SHC2	P98077	528
CIMAP1D	CIB3	Q96Q77	515
CIMAP1D	EML6	Q6ZMW3	515
CIMAP1D	NHLRC4	P0CG21	507
CIMAP1D	TPGS1	Q6ZTW0	506
CIMAP1D	PLCD4	Q9BRC7	489
CIMAP1D	OR2T10	Q8NGZ9	482
CIMAP1D	FAM76A	Q8TAV0	475
CIMAP1D	R3HDM4	Q96D70	474
CIMAP1D	SAXO2	Q658L1	447
CIMAP1D	OR1C1	Q15619	430
CIMAP1D	KCNJ5-AS1	Q8TAV5	420

IntAct

38 interactions, top by confidence:

A	B	Type	Score
HSF2BP	CIMAP1D	psi-mi:“MI:0915”(physical association)	0.560
CASP6	CIMAP1D	psi-mi:“MI:0915”(physical association)	0.560
CHAT	CIMAP1D	psi-mi:“MI:0915”(physical association)	0.560
CIMAP1D	FGFR3	psi-mi:“MI:0915”(physical association)	0.560
CIMAP1D	GFAP	psi-mi:“MI:0915”(physical association)	0.560
HMOX2	CIMAP1D	psi-mi:“MI:0915”(physical association)	0.560
LMNA	CIMAP1D	psi-mi:“MI:0915”(physical association)	0.560
RAN	CIMAP1D	psi-mi:“MI:0915”(physical association)	0.560
CIMAP1D	OPTN	psi-mi:“MI:0915”(physical association)	0.560
CIMAP1D	JPH3	psi-mi:“MI:0915”(physical association)	0.560
CIMAP1D	SPRED1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (25): NMT1 (Affinity Capture-MS), NMT2 (Affinity Capture-MS), GPHN (Affinity Capture-MS), TRAPPC9 (Affinity Capture-MS), FBXW5 (Affinity Capture-MS), ABI1 (Affinity Capture-MS), GPHN (Affinity Capture-MS), NMT2 (Affinity Capture-MS), FBXW5 (Affinity Capture-MS), NMT1 (Affinity Capture-MS), KCTD10 (Affinity Capture-MS), ODF3L2 (Affinity Capture-MS), ODF3L2 (Two-hybrid), NMT2 (Affinity Capture-MS), KCTD10 (Affinity Capture-MS)

ESM2 similar proteins: A1A5R9, A2AVQ5, A2RRW4, A2RSX4, A5WUY6, A9JS51, B0BM24, B0S4Q5, B1H283, D4A039, F1MMV1, Q08BC4, Q0VB26, Q2T9Q3, Q2TA11, Q2TBS4, Q3KQ80, Q3SX64, Q3TZ65, Q3ZCV2, Q4KKZ1, Q4KLY8, Q4R5Y0, Q5PQN4, Q5RAF2, Q5XI56, Q6ZN84, Q810P2, Q8BUG5, Q8C008, Q8C8J0, Q8IXM7, Q8N412, Q8N6G2, Q8N7U6, Q8N801, Q8TCI5, Q8WW14, Q9D067, Q9D131

Diamond homologs: A3KQA5, A8MYP8, Q2TBH0, Q3SX64, Q3TZ65, Q5EB30, Q5M8M2, Q8AVY1, Q8IXM7, Q920N1, Q96PU9, Q2KIH8, Q810P2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	6
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

627 predictions. Top by Δscore:

Variant	Effect	Δscore
19:474651:T:TA	donor_gain	1.0000
19:464365:C:CC	acceptor_gain	0.9900
19:464373:G:C	acceptor_gain	0.9900
19:464373:G:GC	acceptor_gain	0.9900
19:472392:AC:A	donor_gain	0.9900
19:472393:CC:C	donor_gain	0.9900
19:474617:GCA:G	donor_loss	0.9900
19:474618:CACC:C	donor_loss	0.9900
19:474619:A:AC	donor_gain	0.9900
19:474619:ACCG:A	donor_loss	0.9900
19:474620:C:CA	donor_loss	0.9900
19:474620:C:CC	donor_gain	0.9900
19:474620:CCGTT:C	donor_gain	0.9900
19:464364:CCT:C	acceptor_loss	0.9800
19:464365:CTGA:C	acceptor_loss	0.9800
19:464366:T:C	acceptor_loss	0.9800
19:464362:GAC:G	acceptor_gain	0.9700
19:472191:CAA:C	acceptor_gain	0.9700
19:474652:C:A	donor_gain	0.9700
19:464363:AC:A	acceptor_gain	0.9600
19:464364:CC:C	acceptor_gain	0.9600
19:467647:ACC:A	donor_gain	0.9600
19:467648:CCC:C	donor_gain	0.9600
19:474615:ACGC:A	donor_loss	0.9600
19:464360:CGGAC:C	acceptor_gain	0.9500
19:467763:C:CC	acceptor_gain	0.9500
19:467640:AGTAC:A	donor_loss	0.9400
19:467641:GTACT:G	donor_loss	0.9400
19:467642:TACT:T	donor_loss	0.9400
19:467643:AC:A	donor_loss	0.9400

AlphaMissense

1828 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:464048:G:C	F222L	0.969
19:464048:G:T	F222L	0.969
19:464050:A:G	F222L	0.969
19:464285:G:C	F143L	0.953
19:464285:G:T	F143L	0.953
19:464287:A:G	F143L	0.953
19:463940:G:C	F258L	0.940
19:463940:G:T	F258L	0.940
19:463942:A:G	F258L	0.940
19:467701:A:C	F99L	0.928
19:467701:A:T	F99L	0.928
19:467703:A:G	F99L	0.928
19:467743:G:C	S85R	0.925
19:467743:G:T	S85R	0.925
19:467745:T:G	S85R	0.925
19:467699:C:T	G100D	0.896
19:467738:C:T	G87D	0.894
19:464335:A:C	Y127D	0.880
19:464346:C:T	G123D	0.879
19:464046:G:A	T223I	0.877
19:463998:C:T	G239D	0.856
19:467699:C:A	G100V	0.855
19:467679:A:C	Y107D	0.843
19:467739:C:G	G87R	0.817
19:464183:C:A	K177N	0.816
19:464183:C:G	K177N	0.816
19:464106:C:T	G203D	0.801
19:464224:A:C	Y164D	0.800
19:464325:T:A	E130V	0.799
19:467708:G:A	T97I	0.798

dbSNP variants (sampled 300 via entrez): RS1000153545 (19:488994 A>G,T), RS1000267324 (19:469464 T>G), RS1000483064 (19:465140 T>A,C,G), RS1000556166 (19:483718 A>G), RS1000572931 (19:477954 C>T), RS1000575282 (19:478088 G>A), RS1000726699 (19:472362 G>A,T), RS1000757161 (19:489802 G>A), RS1000816498 (19:463999 C>A,T), RS1000965901 (19:469427 C>T), RS1000989795 (19:478736 C>T), RS1001018273 (19:469199 G>A), RS1001102968 (19:490036 G>A), RS1001269009 (19:484202 G>A), RS1001395608 (19:479127 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000904_4	Asperger disorder	5.000000e-06
GCST90002406_517	Reticulocyte fraction of red cells	3.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acid	affects methylation, increases abundance	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	increases methylation	1
ICG 001	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Temozolomide	decreases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Cannabinoids	increases abundance, affects methylation	1
Methapyrilene	increases methylation	1
Plant Extracts	decreases expression, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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