CLMN

Summary

CLMN (calmin, HGNC:19972) is a protein-coding gene on chromosome 14q32.13, encoding Calmin (Q96JQ2).

Predicted to enable actin filament binding activity. Predicted to be involved in negative regulation of cell population proliferation and nuclear migration. Predicted to act upstream of or within neuron projection development. Predicted to be located in membrane. Predicted to be part of meiotic nuclear membrane microtubule tethering complex. Predicted to be active in cytoplasm and nuclear outer membrane.

Source: NCBI Gene 79789 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 220 total
• GTEx eGene: eQTL in 25 tissues, sQTL in 20 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.76 (unconstrained)
• MANE Select transcript: NM_024734
• Notable: 220 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19972
Approved symbol	CLMN
Name	calmin
Location	14q32.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12383, KIAA1188, KIAA0500
Ensembl gene	ENSG00000165959
Ensembl biotype	protein_coding
OMIM	611121
Entrez	79789

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 11 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000298912

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 3, TSL 3: 1, TSL 4: 1, TSL 5: 3

ENST00000298912, ENST00000553733, ENST00000555336, ENST00000555615, ENST00000556416, ENST00000556441, ENST00000556454, ENST00000557215, ENST00000557696, ENST00000869560, ENST00000941995, ENST00000999844, ENST00000999845, ENST00001115243, ENST00001117632, ENST00001117633, ENST00001135505

RefSeq mRNA: 1 — MANE Select: NM_024734 NM_024734

CCDS: CCDS9933

Canonical transcript exons

ENST00000298912 — 13 exons

Exon	Start	End
ENSE00001098464	95215641	95215733
ENSE00001098491	95221691	95221774
ENSE00001098542	95213219	95213409
ENSE00001168923	95210686	95210879
ENSE00001312578	95181940	95191732
ENSE00001327160	95319711	95319908
ENSE00003463993	95230072	95230133
ENSE00003507005	95223760	95223855
ENSE00003526953	95196498	95196694
ENSE00003531313	95194536	95194596
ENSE00003576300	95202838	95204463
ENSE00003628404	95209395	95209477
ENSE00003629809	95193849	95193919

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 98.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.9064 / max 291.2049, expressed in 1232 samples.

Highest expression (Bgee): sperm, male germ cell, lateral nuclear group of thalamus, bronchial epithelial cell, testis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CLMN is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 25 tissues and its splicing (sQTL) in 20 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 45 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	sqtl	6.8e-101	+1.39	14:95193410:C:T
Cells Cultured fibroblasts	eqtl	1.6e-41	-0.70	14:95248214:T:A
Whole Blood	eqtl	3.1e-31	+0.24	14:95185788:T:C
Nerve Tibial	sqtl	4.3e-24	-0.64	14:95231494:A:G
Artery Tibial	eqtl	3.0e-16	+0.23	14:95292804:G:A
Breast Mammary Tissue	sqtl	3.0e-15	-0.58	14:95231494:A:G
Esophagus Mucosa	eqtl	6.7e-14	-0.31	14:95325205:G:C
Adipose Visceral Omentum	sqtl	7.5e-14	-0.54	14:95222622:C:G
Nerve Tibial	eqtl	4.1e-12	+0.27	14:95193431:A:G
Skin Sun Exposed Lower leg	eqtl	4.8e-11	+0.22	14:95193431:A:G
Adipose Subcutaneous	sqtl	4.7e-10	+0.39	14:95193410:C:T
Thyroid	sqtl	1.3e-09	-0.40	14:95222622:C:G
Adipose Subcutaneous	eqtl	7.8e-09	+0.23	14:95193431:A:G
Artery Tibial	sqtl	9.3e-09	-0.50	14:95193410:C:T
Prostate	sqtl	2.1e-07	-0.80	14:95193410:C:T
Liver	sqtl	1.0e-06	-0.75	14:95231217:T:G
Skin Sun Exposed Lower leg	sqtl	5.0e-06	+0.38	14:95193410:C:T
Muscle Skeletal	sqtl	1.0e-05	+0.38	14:95193410:C:T
Pancreas	sqtl	2.2e-05	-0.56	14:95193410:C:T
Colon Transverse	sqtl	3.5e-05	+0.44	14:95193410:C:T

FANTOM5 promoters

3 alternative TSS:

Promoter ID	TPM avg	Samples expressed
144783	8.1433	1180
144782	1.5792	610
144784	0.1839	81

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.86	gold quality
male germ cell	CL:0000015	96.79	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.54	gold quality
bronchial epithelial cell	CL:0002328	95.85	gold quality
left testis	UBERON:0004533	95.58	gold quality
right testis	UBERON:0004534	95.48	gold quality
renal medulla	UBERON:0000362	94.75	gold quality
epithelium of bronchus	UBERON:0002031	94.61	gold quality
corpus callosum	UBERON:0002336	94.35	gold quality
sural nerve	UBERON:0015488	94.14	gold quality
bronchus	UBERON:0002185	94.12	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.28	gold quality
testis	UBERON:0000473	93.27	gold quality
mucosa of sigmoid colon	UBERON:0004993	92.81	gold quality
colonic mucosa	UBERON:0000317	92.37	gold quality
body of pancreas	UBERON:0001150	92.11	gold quality
dorsal plus ventral thalamus	UBERON:0001897	91.73	gold quality
metanephros cortex	UBERON:0010533	90.96	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	90.70	gold quality
globus pallidus	UBERON:0001875	90.58	gold quality
inferior vagus X ganglion	UBERON:0005363	90.44	gold quality
medial globus pallidus	UBERON:0002477	90.34	gold quality
buccal mucosa cell	CL:0002336	90.21	gold quality
nephron tubule	UBERON:0001231	89.99	gold quality
pancreas	UBERON:0001264	89.70	gold quality
inferior olivary complex	UBERON:0002127	89.64	gold quality
kidney	UBERON:0002113	89.20	gold quality
adult mammalian kidney	UBERON:0000082	89.12	gold quality
subthalamic nucleus	UBERON:0001906	89.10	gold quality
lateral globus pallidus	UBERON:0002476	89.09	gold quality
CA1 field of hippocampus	UBERON:0003881	89.08	gold quality
middle frontal gyrus	UBERON:0002702	89.04	gold quality
peripheral nervous system	UBERON:0000010	89.01	gold quality
tibial nerve	UBERON:0001323	89.01	gold quality
rectum	UBERON:0001052	88.83	gold quality
liver	UBERON:0002107	87.99	gold quality
right lobe of liver	UBERON:0001114	87.71	gold quality
caput epididymis	UBERON:0004358	87.66	gold quality
monocyte	CL:0000576	87.56	gold quality
mononuclear cell	CL:0000842	87.47	gold quality
ventral tegmental area	UBERON:0002691	87.47	gold quality
islet of Langerhans	UBERON:0000006	87.45	gold quality
epithelium of nasopharynx	UBERON:0001951	87.45	gold quality
colonic epithelium	UBERON:0000397	87.29	gold quality
mucosa of transverse colon	UBERON:0004991	87.09	gold quality
substantia nigra pars reticulata	UBERON:0001966	87.04	gold quality
leukocyte	CL:0000738	86.93	gold quality
kidney epithelium	UBERON:0004819	86.73	gold quality
omental fat pad	UBERON:0010414	86.68	gold quality
peritoneum	UBERON:0002358	86.67	gold quality
corpus epididymis	UBERON:0004359	86.63	gold quality
right uterine tube	UBERON:0001302	86.61	gold quality
adipose tissue of abdominal region	UBERON:0007808	86.56	gold quality
seminal vesicle	UBERON:0000998	86.38	gold quality
adipose tissue	UBERON:0001013	86.33	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.26	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.23	gold quality
cortex of kidney	UBERON:0001225	86.05	gold quality
subcutaneous adipose tissue	UBERON:0002190	86.02	gold quality
connective tissue	UBERON:0002384	85.62	gold quality
transverse colon	UBERON:0001157	85.46	gold quality
nasal cavity epithelium	UBERON:0005384	85.38	gold quality
medulla oblongata	UBERON:0001896	85.36	gold quality
endocervix	UBERON:0000458	85.26	gold quality
parietal pleura	UBERON:0002400	85.24	gold quality
choroid plexus epithelium	UBERON:0003911	84.96	gold quality
tibia	UBERON:0000979	84.88	gold quality
mammary gland	UBERON:0001911	84.86	gold quality
thoracic mammary gland	UBERON:0005200	84.77	gold quality
minor salivary gland	UBERON:0001830	84.47	gold quality
Ammon’s horn	UBERON:0001954	84.39	gold quality
midbrain	UBERON:0001891	84.21	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.11	gold quality
substantia nigra	UBERON:0002038	83.94	gold quality
spinal cord	UBERON:0002240	83.54	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.53	gold quality
large intestine	UBERON:0000059	83.43	gold quality
substantia nigra pars compacta	UBERON:0001965	83.39	gold quality
colon	UBERON:0001155	83.24	gold quality
superior vestibular nucleus	UBERON:0007227	83.23	gold quality
epithelium of mammary gland	UBERON:0003244	83.17	gold quality
left uterine tube	UBERON:0001303	83.03	gold quality
pleura	UBERON:0000977	83.01	gold quality
putamen	UBERON:0001874	82.95	gold quality
saliva-secreting gland	UBERON:0001044	82.86	gold quality
metanephros	UBERON:0000081	82.78	gold quality
nasal cavity mucosa	UBERON:0001826	82.76	gold quality
calcaneal tendon	UBERON:0003701	82.73	gold quality
intestine	UBERON:0000160	82.65	gold quality
stomach	UBERON:0000945	82.59	gold quality
mouth mucosa	UBERON:0003729	82.53	gold quality
body of stomach	UBERON:0001161	82.48	gold quality
gall bladder	UBERON:0002110	82.45	gold quality
mammary duct	UBERON:0001765	82.39	gold quality
occipital lobe	UBERON:0002021	82.33	gold quality
postcentral gyrus	UBERON:0002581	82.27	gold quality
primary visual cortex	UBERON:0002436	82.25	gold quality
pylorus	UBERON:0001166	82.18	gold quality
ectocervix	UBERON:0012249	82.11	gold quality
parietal lobe	UBERON:0001872	82.01	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	72.68
E-ANND-3	yes	14.73
E-CURD-119	yes	14.03
E-GEOD-134144	yes	7.93
E-ENAD-27	yes	7.08
E-CURD-11	no	113.86

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 78 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Corpus callosum	tissue	63.3
Nucleus accumbens	tissue	50.6
Thalamus	tissue	46.9
Superior colliculi	tissue	42.2
Midbrain	tissue	41.0
Choroid plexus	tissue	39.4
Locus coeruleus	tissue	37.5
Hippocampus	tissue	35.0	not detected
Pons	tissue	33.8
Substantia nigra	tissue	27.7
Postcentral gyrus	tissue	26.3
Putamen	tissue	25.9
Ventral forebrain	tissue	25.8
Testis	tissue	25.1	high
Medulla oblongata	tissue	24.7
Periaqueductal gray	tissue	22.9
Spinal cord	tissue	20.5
Hypothalamus	tissue	19.6
Hippocampal formation	tissue	19.0
Septum	tissue	17.9
Frontal cortex	tissue	13.8
Amygdala	tissue	13.2
Liver	tissue	13.1	medium
Caudate putamen	tissue	12.9
Kidney	tissue	12.4	high
Cerebral cortex	tissue	12.1	low
Retrosplenial cortex	tissue	12.1
Rectum	tissue	12.0	high
Cerebellum	tissue	12.0	medium
Basal ganglia	tissue	11.7	low
Somatosensory cortex	tissue	10.9
Insular cortex	tissue	10.9
Colon	tissue	10.7	high
Adipose tissue	tissue	10.4	not detected
Occipital cortex	tissue	10.3
Pancreas	tissue	9.7	medium
Motor cortex	tissue	9.6
Retina	tissue	9.1
Prefrontal cortex	tissue	8.9
Breast	tissue	8.6	medium
Retrosplenial and cingulate cortex	tissue	8.5
Entorhinal cortex	tissue	8.1
Temporal cortex	tissue	7.2
Epididymis	tissue	7.0	high
Olfactory bulb	tissue	6.9
Stomach 1	tissue	6.8	high
Vagina	tissue	6.4	not detected
Gallbladder	tissue	5.4	high
Tongue	tissue	5.1
Prostate	tissue	5.0	medium
Fallopian tube	tissue	4.8	medium
Seminal vesicle	tissue	4.7	medium
Salivary gland	tissue	4.5	high
Urinary bladder	tissue	4.5	medium
Appendix	tissue	4.0	high
Small intestine	tissue	3.7	low
Cervix	tissue	3.3	medium
Skeletal muscle	tissue	3.1	low
Thyroid gland	tissue	3.1	low
Lung	tissue	2.9	not detected

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Temporal white matter (160.2), Parieto-temporal junction (white matter) (159.1), Corpus callosum, genu (white matter) (127.2), Corpus callosum, splenium (white matter) (126.2), Centromedial thalamic nucleus (114.1).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CLMN by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 306 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
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

Functional genomics

gnomAD constraint: pLI 2.32e-10, LOEUF 0.755, missense Z 1.31 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000298912 — one region, missense o/e 0.94.

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	clmnb	ENSDARG00000043667
danio_rerio	clmna	ENSDARG00000096867
mus_musculus	Clmn	ENSMUSG00000021097
rattus_norvegicus	Clmn	ENSRNOG00000011044

Paralogs (36): SYNE2 (ENSG00000054654), SPTB (ENSG00000070182), ACTN1 (ENSG00000072110), ACTN2 (ENSG00000077522), DSP (ENSG00000096696), DRP2 (ENSG00000102385), SPTBN1 (ENSG00000115306), MACF1 (ENSG00000127603), FLNC (ENSG00000128591), ACTN4 (ENSG00000130402), SYNE1 (ENSG00000131018), MICAL2 (ENSG00000133816), DTNA (ENSG00000134769), MICAL1 (ENSG00000135596), FLNB (ENSG00000136068), SPTBN5 (ENSG00000137877), DTNB (ENSG00000138101), GAS2L3 (ENSG00000139354), DST (ENSG00000151914), UTRN (ENSG00000152818), SPTBN4 (ENSG00000160460), SPTA1 (ENSG00000163554), PKHD1 (ENSG00000170927), SPTBN2 (ENSG00000173898), SYNE3 (ENSG00000176438), PLEC (ENSG00000178209), SMTNL2 (ENSG00000188176), FLNA (ENSG00000196924), SPTAN1 (ENSG00000197694), DMD (ENSG00000198947), PKHD1L1 (ENSG00000205038), DYTN (ENSG00000232125), MICAL3 (ENSG00000243156), ACTN3 (ENSG00000248746), EPPK1 (ENSG00000261150), GAS2L2 (ENSG00000270765)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:2136957) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 1 distinct phenotype terms.

Mouse phenotype (MP)	Records
decreased prepulse inhibition	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Macaca fascicularis	Q2PFV7	99.9%	Diamond
Pongo abelii	Q5RCS6	99.8%	Diamond
Bos taurus	Q3B7N2	99.6%	Diamond
Gallus gallus	P05094	98.3%	Diamond
Cricetulus griseus	Q9JI55	94.7%	Diamond
Canis lupus familiaris	O97592	94.6%	Diamond
Sus scrofa	Q5GN48	94.6%	Diamond
Drosophila melanogaster	Q9VDW6	91.8%	Diamond
Anopheles gambiae	Q7PKQ5	90.1%	Diamond
Dermatophagoides farinae	L7UZ85	80.5%	Diamond
Dictyostelium discoideum	P05095	52.5%	Diamond
Schizosaccharomyces pombe 972h-	O13728	46.6%	Diamond
Caenorhabditis elegans	Q9N4M4	45.6%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
LINC02279	ncRNA	107984637
DICER1	protein-coding	23405
DICER1-AS1	ncRNA	400242
LINC02292	ncRNA	101929080
MIR3173	ncRNA	100422981

Protein

Protein identifiers

Calmin — Q96JQ2 (reviewed: Q96JQ2)

Alternative names: Calponin-like transmembrane domain protein

All UniProt accessions (5): Q96JQ2, G3V3D8, G3V4C0, G3V5E0, G3V5U3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Widely expressed at intermediate level.

RefSeq proteins (1): NP_079010* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001589	Actinin_actin-bd_CS	Conserved_site
IPR001715	CH_dom	Domain
IPR036872	CH_dom_sf	Homologous_superfamily
IPR047826	CLMN_CH_second	Domain
IPR047827	CLMN_CH_first	Domain
IPR052403	LINC-complex_assoc	Family

Pfam: PF00307

UniProt features (35 total): compositionally biased region 13, modified residue 9, region of interest 6, domain 2, sequence conflict 2, chain 1, transmembrane region 1, sequence variant 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96JQ2-F1	52.84	0.18

Human Protein Atlas

Protein class: Predicted membrane proteins, Predicted intracellular proteins, Plasma proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nuclear bodies; cytosol

Antibody reliability (HPA): IH enhanced · IF approved

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 (9)

Type	Positions
Phosphoserine	301, 402, 619, 713, 769, 838, 841, 907
Phosphothreonine	699

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 187 (showing top): TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN, GOBP_NEUROGENESIS, DELYS_THYROID_CANCER_DN, GOBP_NUCLEUS_LOCALIZATION, CAIRO_HEPATOBLASTOMA_UP, GFI1_01, GOMF_ACTIN_BINDING, NRF2_01, GOBP_CELL_PROJECTION_ORGANIZATION, ROSS_AML_WITH_PML_RARA_FUSION, GOBP_ORGANELLE_LOCALIZATION, chr14q32, YNGTTNNNATT_UNKNOWN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, MULLIGHAN_MLL_SIGNATURE_2_DN

GO Biological Process (2): nuclear migration (GO:0007097), negative regulation of cell population proliferation (GO:0008285)

GO Molecular Function (3): actin filament binding (GO:0051015), actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (4): nuclear outer membrane (GO:0005640), cytoplasm (GO:0005737), meiotic nuclear membrane microtubule tethering complex (GO:0034993), membrane (GO:0016020)

GO top-level categories

17 GO namespaces:

Category	Terms
cellular anatomical structure	2
intracellular transport	1
nucleus localization	1
establishment of organelle localization	1
cell population proliferation	1
regulation of cell population proliferation	1
negative regulation of cellular process	1
actin binding	1
protein-containing complex binding	1
cytoskeletal protein binding	1
binding	1
nuclear membrane	1
organelle outer membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
intracellular anatomical structure	1
microtubule organizing center attachment site	1
nuclear membrane microtubule tethering complex	1

Protein interactions and networks

STRING

showing 16 of 472 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLMN	NRAP	Q86VF7	447
CLMN	STRBP	Q96SI9	416
CLMN	KIF6	Q6ZMV9	401
CLMN	PLAC9	Q5JTB6	393
CLMN	EMD	P50402	389
CLMN	COPB1	P53618	386
CLMN	A1CF	Q9NQ94	378
CLMN	ERICH6B	Q5W0A0	374
CLMN	EFL1	Q7Z2Z2	371
CLMN	AFAP1L2	Q8N4X5	370
CLMN	MYO10	Q9HD67	367
CLMN	UBXN7	O94888	362
CLMN	CYP24A1	Q07973	360
CLMN	LPGAT1	Q92604	358
CLMN	UNC5CL	Q8IV45	346
CLMN	LMNA	P02545	346

IntAct

Human interaction partners of CLMN in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

Partner	Interaction type	MIscore	Records
UQCC4	association	0.350	2
FHL1	physical association	0.000	1

BioGRID (103 interactions; top human partners by supporting records): CTNNA1 (Proximity Label-MS; 2 records), CTNNB1 (Proximity Label-MS; 2 records), SEC61B (Proximity Label-MS; 2 records), SEC62 (Proximity Label-MS; 2 records), TCTEX1D2 (Affinity Capture-MS; 2 records), ACTB (Proximity Label-MS), ACTR3 (Proximity Label-MS), ADCY9 (Affinity Capture-MS), AMBRA1 (Proximity Label-MS), ANXA9 (Affinity Capture-MS), AP2M1 (Affinity Capture-MS), ATG16L1 (Proximity Label-MS), ATP2A1 (Proximity Label-MS), C16orf91 (Affinity Capture-MS), CANX (Proximity Label-MS)

Disease & clinical

Genetic variants

Variant evidence for CLMN: 220 ClinVar records (0 pathogenic / likely pathogenic); 10 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	153
Likely benign	29
Benign	15

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 29 predictions of 1,562):

Position(s)	Effect	Δscore	Sites
14:95193321	donor_gain	1.0000
14:95194534–95194535	donor_loss	1.0000	5
14:95194597–95194598	acceptor_loss	1.0000	6
14:95196496–95196497	donor_loss	1.0000	4
14:95196695–95196696	acceptor_loss	1.0000	6
14:95210685	donor_loss	1.0000	2
14:95223857–95223858	acceptor_gain	1.0000	2
14:95319710	donor_loss	1.0000
14:95191564	donor_gain	0.9900
14:95191646	donor_gain	0.9900

AlphaMissense

1,362 missense substitutions predicted likely pathogenic (of 6,681 scored), across 319 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
F92	8	0.976	0.999
F38	8	0.969	0.997
F211	8	0.962	0.996
F221	8	0.958	0.996
F251	8	0.957	0.993
N96	8	0.953	0.997
D268	8	0.950	0.979
D20	8	0.945	0.981
D61	8	0.940	0.987
N133	8	0.933	0.985
D115	8	0.932	0.984
F286	8	0.932	0.996
F9	8	0.929	0.992
D64	8	0.926	0.988
D210	8	0.912	0.980
H89	8	0.905	0.985
F59	8	0.904	0.980
F138	8	0.902	0.975
D7	8	0.896	0.964
N246	8	0.886	0.971

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

4 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	1.95e-07
Kidney Renal Clear Cell Carcinoma (validation)	favorable	1.09e-05
Pancreatic Adenocarcinoma (TCGA)	unfavorable	8.52e-05
Rectum Adenocarcinoma (validation)	unfavorable	0.000669

Disease associations

OMIM: gene MIM:611121 | disease phenotypes:

GWAS associations

10 associations:

Study	Trait	p-value
GCST006190_65	Diastolic blood pressure x smoking status (ever vs never) interaction (2df test)	9e-10
GCST000635_26	Response to statin therapy	2e-8
GCST001915_33	Alzheimer’s disease (cognitive decline)	2e-8
GCST003854_26	Gut microbiota (functional units)	4e-8
GCST000618_26	Response to antipsychotic treatment	2e-7
GCST001585_36	Breast size	8e-7
GCST002805_2	Body mass index	9e-7
GCST010396_252	Gut microbiota (bacterial taxa, hurdle binary method)	2e-6
GCST004068_25	Venous thromboembolism adjusted for sickle cell variant rs77121243-T	5e-6
GCST009391_441	Metabolite levels	7e-6

EFO canonical traits (from GWAS)

5 canonical traits:

EFO ID	Trait name
EFO:0005937	longitudinal BMI measurement
EFO:0007874	gut microbiome measurement
EFO:0006336	diastolic blood pressure
EFO:0006527	smoking status measurement
EFO:0010387	phosphatidylcholine 38:5 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

PharmGKB variant annotations

Per-publication pharmacogenomic findings for this gene (significant associations).

1 published findings:

Variant	Drug(s)	Category	Finding	PMID
rs8014194	atorvastatin, pravastatin, simvastatin	Efficacy	Allele A is associated with change in total cholesterol when treated with atorvastatin, pravastatin or simvastatin.	PMID:20339536

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects cotreatment, decreases expression, affects expression, decreases methylation	5
sodium arsenite	decreases expression, increases expression	5
Benzo(a)pyrene	decreases methylation, increases expression, affects methylation, decreases expression	5
Estradiol	decreases expression, increases reaction, affects cotreatment, increases expression	5
Valproic Acid	affects expression, decreases methylation, increases expression	4
bisphenol S	increases expression, affects cotreatment, decreases expression	3
Air Pollutants	decreases expression, increases abundance, increases expression	3
Calcitriol	increases expression, increases reaction, affects cotreatment	3
Smoke	increases abundance, increases expression, decreases expression	3
Tobacco Smoke Pollution	affects expression, decreases expression	3
Tretinoin	decreases reaction, increases expression, decreases expression	3
trichostatin A	affects expression, increases expression	2
potassium chromate(VI)	affects cotreatment, decreases expression	2
Fulvestrant	increases expression, affects cotreatment, increases methylation	2
Acetaminophen	decreases expression	2
Dexamethasone	increases expression, affects cotreatment, decreases expression	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Cyclosporine	decreases expression	2
Aflatoxin B1	affects expression, increases methylation	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases methylation	1
bufotalin	decreases expression	1
methylmercuric chloride	decreases expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
tris(2-butoxyethyl) phosphate	decreases expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.