PNMA1

Summary

PNMA1 (PNMA family member 1, HGNC:9158) is a protein-coding gene on chromosome 14q24.3, encoding Paraneoplastic antigen Ma1 (Q8ND90).

This gene encodes a neuron- and testis-specific protein that is also expressed in some paraneoplastic syndromes affecting the nervous system. Some patients with neurologic disorders develop antibodies against the protein encoded by this gene. The identification of the antineuronal antibodies in the sera of these patients has facilitated the diagnosis of paraneoplastic neurological disorders and the early detection of the associated tumors.

Source: NCBI Gene 9240 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_006029

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9158
Approved symbol	PNMA1
Name	PNMA family member 1
Location	14q24.3
Locus type	gene with protein product
Status	Approved
Aliases	MA1
Ensembl gene	ENSG00000176903
Ensembl biotype	protein_coding
OMIM	604010
Entrez	9240

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000316836

RefSeq mRNA: 1 — MANE Select: NM_006029 NM_006029

CCDS: CCDS9818

Canonical transcript exons

ENST00000316836 — 1 exons

Exon	Start	End
ENSE00001236700	73711783	73714384

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 52.0527 / max 507.5659, expressed in 1812 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
143979	49.7876	1811
143978	2.2651	1124

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	98.71	gold quality
ventricular zone	UBERON:0003053	98.43	gold quality
superior frontal gyrus	UBERON:0002661	98.15	gold quality
ganglionic eminence	UBERON:0004023	97.95	gold quality
prefrontal cortex	UBERON:0000451	97.94	gold quality
frontal cortex	UBERON:0001870	97.64	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.45	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.33	gold quality
cerebral cortex	UBERON:0000956	97.15	gold quality
primary visual cortex	UBERON:0002436	97.14	gold quality
right frontal lobe	UBERON:0002810	97.14	gold quality
nucleus accumbens	UBERON:0001882	97.05	gold quality
anterior cingulate cortex	UBERON:0009835	96.87	gold quality
hypothalamus	UBERON:0001898	96.45	gold quality
caudate nucleus	UBERON:0001873	96.37	gold quality
brain	UBERON:0000955	96.31	gold quality
putamen	UBERON:0001874	96.08	gold quality
temporal lobe	UBERON:0001871	95.90	gold quality
amygdala	UBERON:0001876	95.87	gold quality
right testis	UBERON:0004534	95.73	gold quality
left testis	UBERON:0004533	95.66	gold quality
Ammon’s horn	UBERON:0001954	95.48	gold quality
cerebellum	UBERON:0002037	95.46	gold quality
cerebellar cortex	UBERON:0002129	95.43	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.43	gold quality
cerebellar hemisphere	UBERON:0002245	95.39	gold quality
substantia nigra	UBERON:0002038	95.34	gold quality
islet of Langerhans	UBERON:0000006	95.25	gold quality
smooth muscle tissue	UBERON:0001135	95.05	gold quality
tibial artery	UBERON:0007610	94.82	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting PNMA1, 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-5011-5P	100.00	83.46	5820
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-410-3P	99.27	69.98	2457
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-146A-3P	99.13	68.99	1881
HSA-MIR-29B-1-5P	98.86	68.35	1364
HSA-MIR-4773	98.35	67.30	1710
HSA-MIR-211-3P	98.14	66.77	1052
HSA-MIR-219B-5P	97.91	65.80	531
HSA-MIR-3921	97.81	67.45	1431
HSA-MIR-4799-3P	97.78	65.97	893
HSA-MIR-562	97.66	65.63	698
HSA-MIR-510-5P	97.66	65.82	916
HSA-MIR-5588-5P	97.46	65.70	913

Literature-anchored findings (GeneRIF, showing 2)

• this study provides evidence that PNMA1 is involved in tumor growth of pancreatic carcinoma (PMID:25120759)
• PNMA2 functions as antagonist of MOAP-1 and PNMA1 through heterodimeric interaction (PMID:27003254)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pnma1	ENSMUSG00000054383
rattus_norvegicus	Pnma1	ENSRNOG00000010553

Paralogs (13): MOAP1 (ENSG00000165943), ZCCHC18 (ENSG00000166707), CCDC8 (ENSG00000169515), ZCCHC12 (ENSG00000174460), PNMA8A (ENSG00000182013), PNMA3 (ENSG00000183837), PNMA5 (ENSG00000198883), PNMA8B (ENSG00000204851), PNMA6E (ENSG00000214897), PNMA6F (ENSG00000225110), PNMA6A (ENSG00000235961), PNMA2 (ENSG00000240694), PNMA8C (ENSG00000277531)

Protein

Protein identifiers

Paraneoplastic antigen Ma1 — Q8ND90 (reviewed: Q8ND90)

Alternative names: 37 kDa neuronal protein, Neuron- and testis-specific protein 1

All UniProt accessions (1): Q8ND90

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Testis- and brain-specific. In some cancer patients, specifically expressed by paraneoplastic tumor cells.

Miscellaneous. Antibodies against PNMA1 are present in sera from patients suffering of paraneoplastic neurological disorders.

Similarity. Belongs to the PNMA family.

RefSeq proteins (1): NP_006020* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026523	PNMA	Family
IPR048270	PNMA_C	Domain
IPR048271	PNMA_N	Domain

Pfam: PF14893, PF20846

UniProt features (3 total): sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8ND90-F1	80.81	0.37

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 139 (showing top): GOBP_INFLAMMATORY_RESPONSE, GCANCTGNY_MYOD_Q6, TAL1ALPHAE47_01, HNF1_Q6, CAGCTG_AP4_Q5, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, NKX61_01, NKX62_Q2, chr14q24, HP1SITEFACTOR_Q6, HFH3_01, GOBP_INFLAMMATORY_RESPONSE_TO_ANTIGENIC_STIMULUS, BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, MYB_Q3

GO Biological Process (2): inflammatory response to antigenic stimulus (GO:0002437), positive regulation of apoptotic process (GO:0043065)

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

GO Cellular Component (3): nucleolus (GO:0005730), cytoplasm (GO:0005737), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
inflammatory response	1
immune response	1
apoptotic process	1
regulation of apoptotic process	1
positive regulation of programmed cell death	1
binding	1
nuclear lumen	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

724 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PNMA1	KCTD20	Q7Z5Y7	512
PNMA1	ZNF253	O75346	495
PNMA1	AMPH	P49418	474
PNMA1	ASB5	Q8WWX0	460
PNMA1	DOCK7	Q96N67	443
PNMA1	YWHAB	P31946	440
PNMA1	TSPAN6	O43657	425
PNMA1	PPP2R1A	P30153	425
PNMA1	ZIC4	Q8N9L1	425
PNMA1	MAGEA3	P43357	424
PNMA1	CDR2L	Q86X02	418
PNMA1	NDRG1	Q92597	418
PNMA1	DNER	Q8NFT8	411
PNMA1	CYFIP2	Q96F07	411
PNMA1	ITGA6	P23229	403
PNMA1	RTL6	Q6ICC9	403

IntAct

643 interactions, top by confidence:

A	B	Type	Score
ZCCHC12	PNMA1	psi-mi:“MI:0915”(physical association)	0.890
PNMA6A	PNMA1	psi-mi:“MI:0915”(physical association)	0.870
PNMA1	PRPF31	psi-mi:“MI:0915”(physical association)	0.860
SDCBP	PNMA1	psi-mi:“MI:0915”(physical association)	0.790
PNMA1	RUSC1	psi-mi:“MI:0915”(physical association)	0.790
SCNM1	PNMA1	psi-mi:“MI:0915”(physical association)	0.790
PNMA1	ZNF581	psi-mi:“MI:0915”(physical association)	0.790
RUSC1	PNMA1	psi-mi:“MI:0915”(physical association)	0.790
PNMA1	SCNM1	psi-mi:“MI:0915”(physical association)	0.790
ZNF581	PNMA1	psi-mi:“MI:0915”(physical association)	0.790
METTL17	PNMA1	psi-mi:“MI:0915”(physical association)	0.780
PNMA1	SPG7	psi-mi:“MI:0915”(physical association)	0.780
PNMA1	METTL17	psi-mi:“MI:0915”(physical association)	0.780
SPG7	PNMA1	psi-mi:“MI:0915”(physical association)	0.780
NTAQ1	PNMA1	psi-mi:“MI:0915”(physical association)	0.760
PNMA1	SNRPB	psi-mi:“MI:0915”(physical association)	0.720
PNMA1	HOXB9	psi-mi:“MI:0915”(physical association)	0.720
PNMA1	TNNI1	psi-mi:“MI:0915”(physical association)	0.720
PNMA1	PSMA1	psi-mi:“MI:0915”(physical association)	0.720
PNMA1	RTP5	psi-mi:“MI:0915”(physical association)	0.720
PNMA1		psi-mi:“MI:0915”(physical association)	0.720
PNMA1	PNMA5	psi-mi:“MI:0915”(physical association)	0.720
SEMA4C	PNMA1	psi-mi:“MI:0915”(physical association)	0.720
PNMA1	SH2D4A	psi-mi:“MI:0915”(physical association)	0.720
PNMA1	MRPL11	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (259): PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid), PNMA1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GUJ8, A1Z651, A6QLK5, G1SRW8, P03330, P03334, P03336, P03340, P03359, P0CG32, P0CW24, P10262, P11227, P11269, P21414, P21416, P26805, P26806, P26807, P27460, P31622, P31623, P31625, P32594, Q08DL1, Q27ID9, Q2F7I9, Q2F7J0, Q2F7J2, Q2F7J3, Q2KIT6, Q5HZA3, Q5R486, Q6PEW1, Q7SVK7, Q8BHK0, Q8C1C8, Q8JZW8, Q8ND90, Q8VD24

Diamond homologs: A0A0J9YX94, A0A0J9YXQ4, A0A1B0GUJ8, A6QLK5, A7E321, P0CG32, P0CW24, Q08DL1, Q2KIT6, Q5HZA3, Q5R6R8, Q6PEW1, Q80VM8, Q86V59, Q8JZW8, Q8ND90, Q8VD24, Q8VHZ4, Q9CZA5, Q9UL41, Q9ULN7, D3YZV8, P62521, Q5DTT8, Q5R486, Q8BHK0, Q8C1C8, Q95KI4, Q96BY2, Q96PV4, Q9ERH6, Q9GMU3, Q9H0W5, Q9UL42

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

41 predictions. Top by Δscore:

Variant	Effect	Δscore
14:73714131:G:A	donor_gain	0.4800
14:73714170:T:TA	donor_gain	0.4500
14:73714079:T:TA	donor_gain	0.4400
14:73713195:T:A	acceptor_gain	0.4300
14:73714113:G:A	donor_gain	0.3800
14:73713468:C:A	donor_gain	0.3700
14:73714351:AGT:A	donor_gain	0.3600
14:73714353:T:TA	donor_gain	0.3600
14:73714039:T:TA	donor_gain	0.3500
14:73714080:C:A	donor_gain	0.3300
14:73713192:G:GT	acceptor_gain	0.3200
14:73713193:A:AA	acceptor_gain	0.3100
14:73713194:A:AA	acceptor_gain	0.3100
14:73714355:C:CT	donor_gain	0.3000
14:73714356:T:TT	donor_gain	0.3000
14:73714190:C:CA	donor_gain	0.2900
14:73713191:T:TG	acceptor_gain	0.2800
14:73713780:T:TA	donor_gain	0.2800
14:73713931:C:CA	acceptor_gain	0.2800
14:73713721:C:CA	donor_gain	0.2600
14:73714082:C:T	acceptor_gain	0.2600
14:73713467:T:TA	donor_gain	0.2500
14:73714223:A:T	acceptor_gain	0.2500
14:73714360:C:T	donor_gain	0.2500
14:73713202:ATCC:A	acceptor_gain	0.2400
14:73714069:AG:A	donor_gain	0.2400
14:73714359:C:CT	donor_gain	0.2300
14:73713075:CTAGG:C	donor_gain	0.2200
14:73713201:TATCC:T	acceptor_gain	0.2200
14:73713688:C:CT	donor_gain	0.2200

AlphaMissense

2308 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:73712929:A:C	F237L	0.996
14:73712929:A:T	F237L	0.996
14:73712931:A:G	F237L	0.996
14:73713475:G:C	F55L	0.995
14:73713475:G:T	F55L	0.995
14:73713477:A:G	F55L	0.995
14:73713148:G:C	F164L	0.992
14:73713148:G:T	F164L	0.992
14:73713150:A:G	F164L	0.992
14:73713572:A:T	V23D	0.992
14:73713378:A:G	W88R	0.989
14:73713378:A:T	W88R	0.989
14:73712891:A:G	F250S	0.988
14:73713149:A:G	F164S	0.988
14:73712890:A:C	F250L	0.987
14:73712890:A:T	F250L	0.987
14:73712892:A:G	F250L	0.987
14:73713563:A:G	I26T	0.987
14:73713035:A:G	L202S	0.986
14:73713446:A:G	L65S	0.986
14:73712846:A:T	V265D	0.984
14:73712931:A:T	F237I	0.982
14:73713046:C:A	K198N	0.981
14:73713046:C:G	K198N	0.981
14:73713337:A:C	F101L	0.981
14:73713337:A:T	F101L	0.981
14:73713339:A:G	F101L	0.981
14:73713376:C:A	W88C	0.981
14:73713376:C:G	W88C	0.981
14:73713023:A:T	L206H	0.979

dbSNP variants (sampled 300 via entrez): RS1000047721 (14:73712248 T>C), RS1000397338 (14:73711969 A>G), RS1000462824 (14:73716361 G>A), RS1001259102 (14:73714046 G>A), RS1001391259 (14:73712383 G>A), RS1001451263 (14:73712347 C>A,T), RS1002470633 (14:73714043 G>T), RS1002708925 (14:73714814 A>G), RS1002763798 (14:73713868 T>C), RS1003337610 (14:73715076 T>G), RS1003737711 (14:73714189 T>G), RS1004003525 (14:73714509 C>G,T), RS1004784458 (14:73716186 G>C), RS1004820836 (14:73714000 T>G), RS1004824601 (14:73711669 C>G)

Disease associations

OMIM: gene MIM:604010 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

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

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

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression, decreases expression	2
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
Valproic Acid	affects expression, decreases expression	2
Aflatoxin B1	affects expression, increases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
resorcinol	increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
(+)-JQ1 compound	increases expression	1
Temozolomide	decreases expression	1
Arsenic Trioxide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants, Occupational	affects expression	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Benztropine	increases expression	1
Chromium	decreases expression	1
Clozapine	increases expression	1
Doxorubicin	increases expression	1
Mercury	decreases expression	1
Potassium Dichromate	decreases expression	1
Quercetin	increases expression	1
Rotenone	decreases expression	1
Sarin	decreases expression, increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1

Clinical trials (associated diseases)

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