NUP62CL

Summary

NUP62CL (nucleoporin 62 C-terminal like, HGNC:25960) is a protein-coding gene on chromosome Xq22.3, encoding Nucleoporin-62 C-terminal-like protein (Q9H1M0).

This gene encodes a protein containing a domain found in nucleoporins which are glycoproteins found in nuclear pore complexes. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 54830 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 72 total
• MANE Select transcript: NM_017681

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25960
Approved symbol	NUP62CL
Name	nucleoporin 62 C-terminal like
Location	Xq22.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20130
Ensembl gene	ENSG00000198088
Ensembl biotype	protein_coding
Entrez	54830

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 nonsense_mediated_decay

ENST00000372466, ENST00000421752, ENST00000432145, ENST00000484614, ENST00000862524

RefSeq mRNA: 1 — MANE Select: NM_017681 NM_017681

CCDS: CCDS14527

Canonical transcript exons

ENST00000372466 — 9 exons

Exon	Start	End
ENSE00000674323	107154096	107154246
ENSE00000866536	107167649	107167784
ENSE00001353419	107193029	107193072
ENSE00001376924	107206273	107206433
ENSE00001928448	107123427	107124332
ENSE00002177399	107175089	107175193
ENSE00003560848	107153454	107153503
ENSE00003671937	107147743	107147809
ENSE00003685522	107153172	107153306

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 89.18.

FANTOM5 (CAGE): breadth broad, TPM avg 5.6285 / max 165.1895, expressed in 718 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200061	3.1277	583
200060	1.2587	401
200057	0.5223	225
200058	0.3677	190
200062	0.2190	114
200059	0.1332	70

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	89.18	gold quality
corpus epididymis	UBERON:0004359	85.79	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.00	gold quality
bronchial epithelial cell	CL:0002328	84.94	gold quality
choroid plexus epithelium	UBERON:0003911	84.92	gold quality
buccal mucosa cell	CL:0002336	84.34	gold quality
cauda epididymis	UBERON:0004360	82.07	gold quality
epithelium of bronchus	UBERON:0002031	81.77	gold quality
bronchus	UBERON:0002185	80.65	gold quality
right testis	UBERON:0004534	78.63	gold quality
left testis	UBERON:0004533	78.17	gold quality
right adrenal gland cortex	UBERON:0035827	78.13	gold quality
testis	UBERON:0000473	77.88	gold quality
left adrenal gland cortex	UBERON:0035825	77.84	gold quality
right adrenal gland	UBERON:0001233	77.50	gold quality
left adrenal gland	UBERON:0001234	77.34	gold quality
caput epididymis	UBERON:0004358	77.30	gold quality
adrenal cortex	UBERON:0001235	76.09	gold quality
adrenal gland	UBERON:0002369	75.78	gold quality
body of pancreas	UBERON:0001150	75.42	gold quality
left lobe of thyroid gland	UBERON:0001120	75.34	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.06	gold quality
thyroid gland	UBERON:0002046	74.81	gold quality
sperm	CL:0000019	74.28	gold quality
ventricular zone	UBERON:0003053	74.03	gold quality
right lobe of thyroid gland	UBERON:0001119	73.67	gold quality
male germ cell	CL:0000015	73.23	gold quality
adrenal tissue	UBERON:0018303	72.18	gold quality
rectum	UBERON:0001052	72.10	gold quality
pancreas	UBERON:0001264	72.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	276.04
E-ANND-3	no	3.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting NUP62CL, 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-3613-3P	100.00	76.36	7965
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-1323	99.83	69.89	2471

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Nup62cl	ENSMUSG00000072944
rattus_norvegicus	Nup62cl	ENSRNOG00000057753

Paralogs (1): NUP62 (ENSG00000213024)

Protein

Protein identifiers

Nucleoporin-62 C-terminal-like protein — Q9H1M0 (reviewed: Q9H1M0)

All UniProt accessions (4): Q9H1M0, A0A0S2Z5E8, H0Y6X7, Q5JSN5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the nucleoporin NSP1/NUP62 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H1M0-1	1	yes
Q9H1M0-2	2

RefSeq proteins (1): NP_060151* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007758	Nucleoporin_NSP1_C	Domain
IPR026010	NSP1/NUP62	Family

Pfam: PF05064

UniProt features (6 total): splice variant 2, sequence variant 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H1M0-F1	75.02	0.47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): GOBP_NUCLEAR_TRANSPORT, DELYS_THYROID_CANCER_DN, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, TGTYNNNNNRGCARM_UNKNOWN, SENESE_HDAC3_TARGETS_DN, GOCC_NUCLEAR_ENVELOPE, GOCC_NUCLEAR_PORE, MYCMAX_03, MAX_01, GOMF_STRUCTURAL_CONSTITUENT_OF_NUCLEAR_PORE, ARNT_01, VECCHI_GASTRIC_CANCER_EARLY_UP, GOMF_STRUCTURAL_MOLECULE_ACTIVITY

GO Biological Process (2): protein transport (GO:0015031), nucleocytoplasmic transport (GO:0006913)

GO Molecular Function (2): structural constituent of nuclear pore (GO:0017056), protein binding (GO:0005515)

GO Cellular Component (2): nuclear pore (GO:0005643), nuclear envelope (GO:0005635)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
intracellular protein localization	1
establishment of protein localization	1
nuclear transport	1
structural molecule activity	1
nuclear pore	1
nucleocytoplasmic transport	1
binding	1
nuclear envelope	1
nuclear protein-containing complex	1
nucleus	1
endomembrane system	1
organelle envelope	1

Protein interactions and networks

STRING

566 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUP62CL	OR5AP2	Q8NGF4	517
NUP62CL	OR1L8	Q8NGR8	501
NUP62CL	NUP210L	Q5VU65	498
NUP62CL	NUP153	P49790	487
NUP62CL	FOXD4L6	Q3SYB3	480
NUP62CL	OR8B4	Q96RC9	479
NUP62CL	FBXO48	Q5FWF7	473
NUP62CL	DNAAF6	Q9NQM4	473
NUP62CL	NUP93	Q8N1F7	452
NUP62CL	ZNF684	Q5T5D7	449
NUP62CL	NUP107	P57740	442
NUP62CL	NUP98	P52948	440
NUP62CL	NUP50	Q9UKX7	438
NUP62CL	NUP205	Q92621	436
NUP62CL	NUP155	O75694	435

IntAct

41 interactions, top by confidence:

A	B	Type	Score
OGT	NUP62CL	psi-mi:“MI:0915”(physical association)	0.740
NUP62CL	OGT	psi-mi:“MI:0915”(physical association)	0.740
NUP62CL	OGT	psi-mi:“MI:0914”(association)	0.740
AGR2	NUP62CL	psi-mi:“MI:0915”(physical association)	0.720
NUP62CL	OGT	psi-mi:“MI:0915”(physical association)	0.560
POU6F2	NUP62CL	psi-mi:“MI:0915”(physical association)	0.560
	NUP62CL	psi-mi:“MI:0915”(physical association)	0.560
SNAPIN	NUP62CL	psi-mi:“MI:0915”(physical association)	0.560
NUP62CL	NUP54	psi-mi:“MI:0915”(physical association)	0.550
NUP62CL	DVL2	psi-mi:“MI:0915”(physical association)	0.490
DVL2	NUP62CL	psi-mi:“MI:0915”(physical association)	0.490
NUP62CL	NUP54	psi-mi:“MI:0915”(physical association)	0.370
NUP62CL	PB2	psi-mi:“MI:0915”(physical association)	0.370
ECE1	NUP62CL	psi-mi:“MI:0915”(physical association)	0.370
NUP54	LPXN	psi-mi:“MI:0914”(association)	0.350
NUP88	NUP214	psi-mi:“MI:0914”(association)	0.350
NUP58	RNF40	psi-mi:“MI:0914”(association)	0.350
MXD3	SAP30	psi-mi:“MI:0914”(association)	0.350
CFAP184	TARS3	psi-mi:“MI:0914”(association)	0.350
NUP62CL	WASH3P	psi-mi:“MI:0914”(association)	0.350

BioGRID (46): NUP62CL (Two-hybrid), NUP62CL (Two-hybrid), NUP62CL (Two-hybrid), NUP62CL (Affinity Capture-MS), NUP62CL (Affinity Capture-MS), NUP62CL (Affinity Capture-MS), NUP62CL (Affinity Capture-MS), DVL2 (Two-hybrid), OGT (Two-hybrid), NUP62CL (Synthetic Lethality), NUP62CL (Two-hybrid), NUP62CL (Two-hybrid), NUP62CL (Two-hybrid), NUP62CL (Two-hybrid), NUP62CL (Two-hybrid)

ESM2 similar proteins: A0A2K5V015, A1A4Y4, A4QPB2, A6MMD4, B1AUS7, B2KG20, C0HJZ2, C9J202, F4HT77, F4JGB7, O43423, O43908, O60384, O81514, P06017, P07209, P0C5K4, P0DJ43, P15773, P18269, P18270, P25713, P37360, P51421, P55944, P64936, P81044, P82810, P86265, P86971, P9WLJ8, P9WLJ9, Q03877, Q07444, Q2PFZ0, Q2PS21, Q49744, Q5IAA9, Q5R6R1, Q5T1H1

Diamond homologs: G0SBQ3, P14907, Q9H1M0, P17955, P37198, Q10168, Q63850, Q7JXF5, Q8L7F7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1664 predictions. Top by Δscore:

Variant	Effect	Δscore
X:107124328:CATGC:C	acceptor_gain	1.0000
X:107124329:ATGC:A	acceptor_gain	1.0000
X:107124330:TGC:T	acceptor_gain	1.0000
X:107124331:GC:G	acceptor_gain	1.0000
X:107124332:CC:C	acceptor_gain	1.0000
X:107124333:C:CC	acceptor_gain	1.0000
X:107124333:CT:C	acceptor_loss	1.0000
X:107124334:T:C	acceptor_loss	1.0000
X:107153166:ACTT:A	donor_loss	1.0000
X:107153168:TTA:T	donor_loss	1.0000
X:107153169:TACAT:T	donor_loss	1.0000
X:107153170:A:AC	donor_gain	1.0000
X:107153170:ACA:A	donor_loss	1.0000
X:107153171:C:CA	donor_gain	1.0000
X:107153171:C:G	donor_loss	1.0000
X:107153171:CA:C	donor_gain	1.0000
X:107153171:CAT:C	donor_gain	1.0000
X:107153171:CATCT:C	donor_gain	1.0000
X:107153302:CCAAT:C	acceptor_gain	1.0000
X:107153303:CAATC:C	acceptor_gain	1.0000
X:107153307:C:CC	acceptor_gain	1.0000
X:107153311:A:AC	acceptor_gain	1.0000
X:107153504:C:CC	acceptor_gain	1.0000
X:107154091:CTTAC:C	donor_loss	1.0000
X:107154092:TTA:T	donor_loss	1.0000
X:107154095:CCAT:C	donor_gain	1.0000
X:107154242:CTACA:C	acceptor_gain	1.0000
X:107154245:CA:C	acceptor_gain	1.0000
X:107154247:C:CC	acceptor_gain	1.0000
X:107167643:GCTTA:G	donor_loss	1.0000

AlphaMissense

1192 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:107153460:T:G	Q130P	0.970
X:107154146:C:G	A99P	0.946
X:107154156:A:C	F95L	0.935
X:107154156:A:T	F95L	0.935
X:107154158:A:G	F95L	0.935
X:107153271:T:G	Q144P	0.931
X:107153304:A:G	L133S	0.912
X:107154178:A:G	L88P	0.905
X:107153274:T:G	Q143P	0.904
X:107153262:A:G	L147P	0.903
X:107154191:A:G	W84R	0.894
X:107154191:A:T	W84R	0.894
X:107153285:A:C	F139L	0.879
X:107153285:A:T	F139L	0.879
X:107153287:A:G	F139L	0.879
X:107154157:A:G	F95S	0.858
X:107153280:A:G	L141P	0.846
X:107154169:T:G	Q91P	0.839
X:107154131:C:G	A104P	0.838
X:107154189:C:A	W84C	0.835
X:107154189:C:G	W84C	0.835
X:107154211:A:G	L77P	0.835
X:107153502:A:G	I116T	0.832
X:107154136:A:T	V102D	0.831
X:107154115:A:G	L109S	0.817
X:107153493:A:G	L119S	0.816
X:107154148:T:G	Q98P	0.794
X:107153499:C:G	R117P	0.792
X:107154145:G:T	A99D	0.791
X:107154154:A:G	L96P	0.790

dbSNP variants (sampled 300 via entrez): RS1000023506 (X:107197931 T>C), RS1000086303 (X:107152778 A>T), RS1000134532 (X:107186727 G>A), RS1000219048 (X:107138513 G>A), RS1000256268 (X:107195193 A>G), RS1000314060 (X:107204721 T>A,C), RS1000341856 (X:107177096 A>G), RS1000365088 (X:107204425 C>T), RS1000386938 (X:107132553 G>A), RS1000482013 (X:107130032 C>G), RS1000525696 (X:107144178 C>A,G), RS1000578029 (X:107143756 C>T), RS1000791206 (X:107168499 T>C), RS1000799884 (X:107161741 A>G), RS1000825689 (X:107169404 T>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

4 associations (top):

Study	Trait	p-value
GCST004860_127	Alcoholic chronic pancreatitis	7.000000e-06
GCST004860_82	Alcoholic chronic pancreatitis	1.000000e-32
GCST004860_84	Alcoholic chronic pancreatitis	2.000000e-17
GCST004860_85	Alcoholic chronic pancreatitis	1.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	7
Benzo(a)pyrene	affects methylation, increases expression	3
Cyclosporine	increases expression, decreases expression	3
Aflatoxin B1	increases methylation, affects expression, increases expression	3
Acetaminophen	increases expression, decreases expression	2
Arsenic	increases methylation, decreases expression, increases abundance	2
Cadmium	decreases expression, increases abundance	2
Calcitriol	decreases expression, increases expression, affects cotreatment	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
sodium arsenate	decreases expression, increases abundance	1
beta-lapachone	increases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	increases expression, affects cotreatment	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
torcetrapib	increases expression	1
dorsomorphin	increases expression, affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Ethanol	increases expression	1
Carbamazepine	affects expression	1
Cisplatin	affects cotreatment, increases expression	1
Coumestrol	affects cotreatment, increases expression	1
Methotrexate	increases expression	1
Quercetin	increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, decreases expression	1
Thiram	decreases expression	1

Clinical trials (associated diseases)

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