CIMIP7

Summary

CIMIP7 (ciliary microtubule inner protein 7, HGNC:44666) is a protein-coding gene on chromosome 3p21.31, encoding Ciliary microtubule inner protein 7 (H3BNL1).

Predicted to be located in cilium.

Source: NCBI Gene 646498 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001080528

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44666
Approved symbol	CIMIP7
Name	ciliary microtubule inner protein 7
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000236980
Ensembl biotype	protein_coding
Entrez	646498

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000432035, ENST00000443990, ENST00000545770

RefSeq mRNA: 1 — MANE Select: NM_001080528 NM_001080528

CCDS: CCDS58831

Canonical transcript exons

ENST00000545770 — 4 exons

Exon	Start	End
ENSE00002261300	49191745	49191858
ENSE00002281727	49190025	49190138
ENSE00002608746	49177634	49178052
ENSE00003631782	49178482	49178538

Expression profiles

Bgee: expression breadth broad, 19 present calls, max score 88.32.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.32	gold quality
right testis	UBERON:0004534	72.68	gold quality
left testis	UBERON:0004533	72.61	gold quality
testis	UBERON:0000473	71.86	gold quality
adrenal tissue	UBERON:0018303	53.04	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	51.72	silver quality
granulocyte	CL:0000094	39.87	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
sural nerve	UBERON:0015488	35.90	gold quality
mucosa of stomach	UBERON:0001199	35.59	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
tonsil	UBERON:0002372	32.91	gold quality
leukocyte	CL:0000738	32.57	silver quality
monocyte	CL:0000576	32.33	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
liver	UBERON:0002107	30.86	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
urinary bladder	UBERON:0001255	29.28	gold quality
prefrontal cortex	UBERON:0000451	29.24	gold quality
lymph node	UBERON:0000029	29.22	silver quality
adrenal gland	UBERON:0002369	28.65	silver quality
duodenum	UBERON:0002114	28.14	gold quality
placenta	UBERON:0001987	28.13	gold quality
muscle of leg	UBERON:0001383	27.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	BC048562	ENSMUSG00000050641

Protein

Protein identifiers

Ciliary microtubule inner protein 7 — H3BNL1 (reviewed: H3BNL1)

All UniProt accessions (2): H3BNL1, H3BQU4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell projection. Cilium.

RefSeq proteins (1): NP_001073997* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029369	HDNR	Domain

Pfam: PF15115

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H3BNL1-F1	58.39	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): GOCC_CILIUM, chr3p21, GSE14415_INDUCED_TREG_VS_FOXP3_KO_INDUCED_TREG_IL2_CULTURE_DN, DESCARTES_MAIN_FETAL_CSH1_CSH2_POSITIVE_CELLS, GSE26669_CD4_VS_CD8_TCELL_IN_MLR_COSTIM_BLOCK_UP, GSE27786_BCELL_VS_ERYTHROBLAST_DN, GSE30962_ACUTE_VS_CHRONIC_LCMV_SECONDARY_INF_CD8_TCELL_UP, GSE32423_CTRL_VS_IL7_MEMORY_CD8_TCELL_UP, GSE39820_TGFBETA1_VS_TGFBETA3_IN_IL6_IL23A_TREATED_CD4_TCELL_DN, GSE4984_GALECTIN1_VS_LPS_STIM_DC_DN, GSE5589_LPS_AND_IL10_VS_LPS_AND_IL6_STIM_IL10_KO_MACROPHAGE_45MIN_UP, GSE6259_33D1_POS_DC_VS_CD8_TCELL_UP, GSE20198_UNTREATED_VS_IL12_TREATED_ACT_CD4_TCELL_DN, GSE37605_TREG_VS_TCONV_C57BL6_FOXP3_IRES_GFP_UP, GSE37605_C57BL6_VS_NOD_FOXP3_IRES_GFP_TREG_UP

GO Biological Process (1): biological_process (GO:0008150)

GO Molecular Function (1): molecular_function (GO:0003674)

GO Cellular Component (3): cilium (GO:0005929), cellular_component (GO:0005575), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cellular anatomical structure	1

Protein interactions and networks

STRING

50 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMIP7	TYW3	Q6IPR3	570
CIMIP7	PRRC2C	Q9Y520	507
CIMIP7	SLC44A5	Q8NCS7	507
CIMIP7	ANO10	Q9NW15	476
CIMIP7	ASXL3	Q9C0F0	435
CIMIP7	CRYZ	Q08257	259
CIMIP7	MS4A15	Q8N5U1	244
CIMIP7	TECPR2	O15040	238
CIMIP7	DRD2	P14416	213
CIMIP7	CTSV	O60911	195
CIMIP7	ABHD13	Q7L211	181
CIMIP7	PAFAH1B1	P43034	181
CIMIP7	RPP25	Q9BUL9	162
CIMIP7	NCKAP5L	Q9HCH0	0
CIMIP7	IGSF8	Q969P0	0
CIMIP7	ACKR1	Q16570	0
CIMIP7	AVPI1	Q5T686	0

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A087WRI3, A2AIP0, A2RRW4, A4D2P6, A6QPC0, A8E5W8, A8MTA8, A9JS51, E9PGG2, G3X6E2, H3BNL1, O08856, O43247, O43566, O70373, P54098, P54099, Q0VB26, Q12770, Q2TA11, Q2TBR5, Q3ZBN4, Q400G9, Q4QR77, Q5MNU5, Q5RDC3, Q6J272, Q6ZQR2, Q70EL4, Q8BL74, Q8BUM9, Q8BX43, Q8C0R7, Q8C4S8, Q8N1D5, Q8N6G2, Q8WUA4, Q8WW14, Q969Z4, Q96MK2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

977 predictions. Top by Δscore:

Variant	Effect	Δscore
3:49178463:T:TA	donor_gain	1.0000
3:49178480:A:AC	donor_gain	1.0000
3:49178481:C:CC	donor_gain	1.0000
3:49178538:CCT:C	acceptor_gain	1.0000
3:49178540:T:C	acceptor_gain	1.0000
3:49178540:T:TC	acceptor_gain	1.0000
3:49178411:CCAT:C	donor_gain	0.9900
3:49178431:T:TA	donor_gain	0.9900
3:49178451:G:GA	donor_gain	0.9900
3:49178536:CTC:C	acceptor_gain	0.9900
3:49178539:C:A	acceptor_loss	0.9900
3:49178539:C:CC	acceptor_gain	0.9900
3:49178548:CAG:C	acceptor_gain	0.9900
3:49178550:G:C	acceptor_gain	0.9900
3:49178550:G:GC	acceptor_gain	0.9900
3:49178434:G:C	donor_gain	0.9800
3:49178549:A:T	acceptor_gain	0.9800
3:49191757:TAAAG:T	donor_gain	0.9800
3:49178030:CC:C	acceptor_gain	0.9700
3:49178031:CC:C	acceptor_gain	0.9700
3:49178473:GGCAC:G	donor_loss	0.9700
3:49178474:GCACT:G	donor_loss	0.9700
3:49178475:CACT:C	donor_loss	0.9700
3:49178476:AC:A	donor_loss	0.9700
3:49178477:CT:C	donor_loss	0.9700
3:49178478:TCACT:T	donor_loss	0.9700
3:49178479:C:CC	donor_loss	0.9700
3:49178480:AC:A	donor_loss	0.9700
3:49178481:C:G	donor_loss	0.9700
3:49178537:TC:T	acceptor_gain	0.9700

AlphaMissense

1332 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:49190124:G:C	F14L	0.957
3:49190124:G:T	F14L	0.957
3:49190126:A:G	F14L	0.957
3:49190040:G:C	F42L	0.910
3:49190040:G:T	F42L	0.910
3:49190042:A:G	F42L	0.910
3:49177813:G:C	F146L	0.901
3:49177813:G:T	F146L	0.901
3:49177815:A:G	F146L	0.901
3:49178515:G:C	F55L	0.895
3:49178515:G:T	F55L	0.895
3:49178517:A:G	F55L	0.895
3:49177981:G:C	F90L	0.877
3:49177981:G:T	F90L	0.877
3:49177983:A:G	F90L	0.877
3:49177861:A:C	F130L	0.871
3:49177861:A:T	F130L	0.871
3:49177863:A:G	F130L	0.871
3:49178488:A:C	F64L	0.871
3:49178488:A:T	F64L	0.871
3:49178490:A:G	F64L	0.871
3:49177909:G:C	F114L	0.869
3:49177909:G:T	F114L	0.869
3:49177911:A:G	F114L	0.869
3:49191745:C:A	W9C	0.855
3:49191745:C:G	W9C	0.855
3:49177974:A:G	W93R	0.849
3:49177974:A:T	W93R	0.849
3:49191747:A:G	W9R	0.846
3:49191747:A:T	W9R	0.846

dbSNP variants (sampled 300 via entrez): RS1000029994 (3:49179011 G>A,T), RS1000630932 (3:49181140 G>A), RS1000747026 (3:49180901 G>A), RS1001088375 (3:49177214 C>G), RS1001249184 (3:49191347 A>T), RS1001256474 (3:49185892 A>C,G), RS1001304427 (3:49183014 C>A,T), RS1001637287 (3:49189977 G>A,T), RS1001698859 (3:49190973 G>A), RS1001919757 (3:49189474 C>T), RS1002427867 (3:49182932 G>A), RS1003248494 (3:49188174 C>A), RS1003519490 (3:49179440 T>A,C), RS1003763941 (3:49184066 T>A), RS1003882192 (3:49180177 G>A)

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

8 associations (top):

Study	Trait	p-value
GCST004131_23	Inflammatory bowel disease	1.000000e-33
GCST004132_17	Crohn’s disease	3.000000e-23
GCST004133_11	Ulcerative colitis	8.000000e-20
GCST010698_80	Subcortical volume (min-P)	3.000000e-24
GCST010699_110	Brain morphology (min-P)	4.000000e-08
GCST010701_52	Cortical surface area (MOSTest)	1.000000e-16
GCST010702_36	Subcortical volume (MOSTest)	1.000000e-10
GCST010703_262	Brain morphology (MOSTest)	2.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aflatoxin B2	increases methylation	1
Benzo(a)pyrene	affects methylation	1

Clinical trials (associated diseases)

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