PNMA5

Summary

PNMA5 (PNMA family member 5, HGNC:18743) is a protein-coding gene on chromosome Xq28, encoding Paraneoplastic antigen-like protein 5 (Q96PV4).

This gene encodes a member of the paraneoplastic Ma antigen protein family. These proteins have been implicated in the development of paraneoplastic disorders resulting from an immune response directed against them. Paraneoplastic disorders are the result of an abnormal immune response to a tumor. Multiple alternatively spliced variants, encoding the same protein, have been identified.

Source: NCBI Gene 114824 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 35 total — 1 pathogenic
• MANE Select transcript: NM_001184924

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18743
Approved symbol	PNMA5
Name	PNMA family member 5
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1934
Ensembl gene	ENSG00000198883
Ensembl biotype	protein_coding
OMIM	300916
Entrez	114824

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000361887, ENST00000439251, ENST00000452693, ENST00000535214

RefSeq mRNA: 4 — MANE Select: NM_001184924 NM_001103150, NM_001103151, NM_001184924, NM_052926

CCDS: CCDS14718

Canonical transcript exons

ENST00000535214 — 4 exons

Exon	Start	End
ENSE00001724827	152992657	152992786
ENSE00001767428	152991902	152991977
ENSE00001820217	152988824	152991721
ENSE00002275980	152994033	152994116

Expression profiles

Bgee: expression breadth broad, 51 present calls, max score 81.63.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.2213 / max 563.9443, expressed in 68 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200859	0.7044	13
200860	0.2519	12
200858	0.1298	47
200857	0.1229	47
209869	0.0122	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hypothalamus	UBERON:0001898	81.63	gold quality
nucleus accumbens	UBERON:0001882	80.07	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.75	gold quality
superior frontal gyrus	UBERON:0002661	78.00	gold quality
anterior cingulate cortex	UBERON:0009835	76.90	gold quality
temporal lobe	UBERON:0001871	75.31	gold quality
amygdala	UBERON:0001876	75.16	gold quality
right testis	UBERON:0004534	74.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.44	gold quality
Brodmann (1909) area 9	UBERON:0013540	73.93	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	73.88	gold quality
testis	UBERON:0000473	73.61	gold quality
right frontal lobe	UBERON:0002810	73.53	gold quality
left testis	UBERON:0004533	72.92	gold quality
cerebral cortex	UBERON:0000956	71.71	gold quality
frontal cortex	UBERON:0001870	71.04	gold quality
Ammon’s horn	UBERON:0001954	68.83	gold quality
prefrontal cortex	UBERON:0000451	68.49	gold quality
brain	UBERON:0000955	61.62	gold quality
colonic epithelium	UBERON:0000397	61.31	silver quality
cortical plate	UBERON:0005343	60.66	gold quality
monocyte	CL:0000576	59.74	gold quality
leukocyte	CL:0000738	59.01	gold quality
substantia nigra	UBERON:0002038	54.43	gold quality
bone marrow cell	CL:0002092	52.58	gold quality
pituitary gland	UBERON:0000007	51.40	gold quality
spleen	UBERON:0002106	50.39	gold quality
caudate nucleus	UBERON:0001873	50.06	gold quality
primary visual cortex	UBERON:0002436	49.63	gold quality
granulocyte	CL:0000094	48.73	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting PNMA5, 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-5193	100.00	67.26	1744
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-548AV-3P	99.43	68.50	1721
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-877-3P	99.09	68.10	1637
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-6749-3P	99.00	65.73	1443
HSA-MIR-4738-3P	98.98	67.98	1846
HSA-MIR-4724-5P	98.87	67.75	1324
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-6792-3P	98.41	66.86	1359
HSA-MIR-4691-5P	98.41	66.77	1343
HSA-MIR-4704-3P	98.28	69.33	1300
HSA-MIR-93-3P	98.15	66.65	1309
HSA-MIR-660-3P	98.14	66.04	1434
HSA-MIR-4691-3P	98.11	66.83	1204
HSA-MIR-4456	97.50	64.88	1678
HSA-MIR-1913	97.07	66.20	1417
HSA-MIR-514A-5P	96.94	65.49	801
HSA-MIR-874-5P	96.93	63.92	1014

Literature-anchored findings (GeneRIF, showing 1)

• PNMA5 promotes apoptosis signaling in HeLa and MCF-7 cells and interacts synergistically with MOAP-1 through its N-terminal domain to promote apoptosis and chemo-sensitivity in human cancer cells. The C-terminal domain of PNMA5 is required for nuclear localization; however, both N-and C-terminal domains of PNMA5 appear to be required for pro-apoptotic function. (PMID:27424190)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pnma5	ENSMUSG00000050424
rattus_norvegicus	Pnma5	ENSRNOG00000058423

Paralogs (13): MOAP1 (ENSG00000165943), ZCCHC18 (ENSG00000166707), CCDC8 (ENSG00000169515), ZCCHC12 (ENSG00000174460), PNMA1 (ENSG00000176903), PNMA8A (ENSG00000182013), PNMA3 (ENSG00000183837), PNMA8B (ENSG00000204851), PNMA6E (ENSG00000214897), PNMA6F (ENSG00000225110), PNMA6A (ENSG00000235961), PNMA2 (ENSG00000240694), PNMA8C (ENSG00000277531)

Protein

Protein identifiers

Paraneoplastic antigen-like protein 5 — Q96PV4 (reviewed: Q96PV4)

Alternative names: Tumor antigen BJ-HCC-25

All UniProt accessions (1): Q96PV4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Expressed in the brain.

Similarity. Belongs to the PNMA family.

RefSeq proteins (4): NP_001096620, NP_001096621, NP_001171853, NP_443158 (=MANE)

Domains & families (InterPro)

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

Pfam: PF14893, PF20846

UniProt features (10 total): compositionally biased region 3, sequence conflict 3, sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96PV4-F1	70.46	0.11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_UP, MARTENS_TRETINOIN_RESPONSE_UP, chrXq28, PASINI_SUZ12_TARGETS_UP, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, MIR877_3P, MIR5193, MIR5006_5P, MIR1913, MIR6499_3P, GSE11924_TH1_VS_TH2_CD4_TCELL_DN, MIR514A_5P, GSE9946_MATURE_STIMULATORY_VS_PROSTAGLANDINE2_TREATED_MATURE_DC_UP, GSE12963_UNINF_VS_ENV_AND_NEF_DEFICIENT_HIV1_INF_CD4_TCELL_UP

GO Biological Process (1): positive regulation of apoptotic process (GO:0043065)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
apoptotic process	1
regulation of apoptotic process	1
positive regulation of programmed cell death	1
protein binding	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

574 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PNMA5	ZNF251	Q9BRH9	559
PNMA5	CDR2L	Q86X02	544
PNMA5	ZIK1	Q3SY52	534
PNMA5	WFDC12	Q8WWY7	530
PNMA5	ZNF426	Q9BUY5	518
PNMA5	REG1B	P48304	448
PNMA5	RTL5	Q5HYW3	409
PNMA5	CLPSL1	A2RUU4	394
PNMA5	LDOC1	O95751	391
PNMA5	RFPL4B	Q6ZWI9	377
PNMA5	RTL1	A6NKG5	369
PNMA5	HOXC13	P31276	360
PNMA5	RTL3	Q8N8U3	353
PNMA5	LAMA3	Q16787	349
PNMA5	PEG10	Q86TG7	335

IntAct

247 interactions, top by confidence:

A	B	Type	Score
PNMA5	ARPC4	psi-mi:“MI:0915”(physical association)	0.780
PNMA5	NTAQ1	psi-mi:“MI:0915”(physical association)	0.780
GORASP2	PNMA5	psi-mi:“MI:0915”(physical association)	0.780
ARPC4	PNMA5	psi-mi:“MI:0915”(physical association)	0.780
NTAQ1	PNMA5	psi-mi:“MI:0915”(physical association)	0.780
PNMA5	GORASP2	psi-mi:“MI:0915”(physical association)	0.780
PNMA5	CCDC102B	psi-mi:“MI:0915”(physical association)	0.720
RAD23B	PNMA5	psi-mi:“MI:0915”(physical association)	0.720
PNMA5	ZMYND19	psi-mi:“MI:0915”(physical association)	0.720
VIM	PNMA5	psi-mi:“MI:0915”(physical association)	0.720
PNMA1	PNMA5	psi-mi:“MI:0915”(physical association)	0.720
CCDC102B	PNMA5	psi-mi:“MI:0915”(physical association)	0.720
ZMYND19	PNMA5	psi-mi:“MI:0915”(physical association)	0.720
PNMA5	VIM	psi-mi:“MI:0915”(physical association)	0.720
PNMA5	PNMA1	psi-mi:“MI:0915”(physical association)	0.720
PNMA5	RAD23B	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (80): PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid), PNMA5 (Two-hybrid)

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A5D7L8, A6NDY0, A6NKD2, A7E321, E9PGG2, F6SZT2, O14771, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P17564, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q2M329, Q587J8, Q5DTT8, Q5R5G8, Q5R6R8, Q5SV97, Q60465, Q62881, Q69ZB3, Q6P752, Q86V59, Q8BSI6, Q8IWY8, Q8N3D4, Q8VD63

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	18
Likely benign	4
Benign	4

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
144336	GRCh38/hg38 Xq27.1-28(chrX:139333024-155978689)x1	Pathogenic

SpliceAI

240 predictions. Top by Δscore:

Variant	Effect	Δscore
X:152991906:C:CA	donor_gain	1.0000
X:152991917:T:TA	donor_gain	1.0000
X:152991901:CCA:C	donor_gain	0.9900
X:152991920:T:TA	donor_gain	0.9900
X:152991936:T:TA	donor_gain	0.9900
X:152992076:A:AC	donor_gain	0.9800
X:152992077:C:CC	donor_gain	0.9800
X:152992112:T:TA	donor_gain	0.9800
X:152991913:G:T	donor_gain	0.9700
X:152991914:A:AC	donor_gain	0.9700
X:152991915:C:CC	donor_gain	0.9700
X:152991918:C:A	donor_gain	0.9700
X:152992069:A:AC	donor_gain	0.9700
X:152992070:C:CC	donor_gain	0.9700
X:152991901:CCACT:C	donor_gain	0.9600
X:152991718:CAGC:C	acceptor_gain	0.9500
X:152991896:TCTCA:T	donor_loss	0.9400
X:152991899:CACCA:C	donor_loss	0.9400
X:152991900:ACC:A	donor_loss	0.9400
X:152991914:ACTT:A	donor_gain	0.9400
X:152991915:CTTC:C	donor_gain	0.9400
X:152992077:CT:C	donor_gain	0.9400
X:152992105:AGCAC:A	donor_gain	0.9400
X:152991895:ATCTC:A	donor_loss	0.9300
X:152991916:T:C	donor_gain	0.9300
X:152991876:C:A	donor_gain	0.9200
X:152992070:CTG:C	donor_gain	0.9200
X:152991894:CATCT:C	donor_loss	0.9100
X:152991900:A:AC	donor_gain	0.9100
X:152991901:C:CC	donor_gain	0.9100

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000683248 (X:152996029 G>A,C), RS1004090399 (X:152990181 A>C), RS1004337877 (X:152989549 C>T), RS1005594896 (X:152991784 C>T), RS1006771799 (X:152992374 G>A), RS1008185105 (X:152990329 G>A), RS1008598540 (X:152994090 G>A,T), RS1011414744 (X:152993115 C>T), RS1011467312 (X:152992835 C>T), RS1013039248 (X:152993630 C>T), RS1014304373 (X:152994921 T>G), RS1014769827 (X:152994519 T>G), RS1015355784 (X:152989566 C>T), RS1016053644 (X:152993632 C>T), RS1016307711 (X:152993343 C>G)

Disease associations

OMIM: gene MIM:300916 | 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

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation	1
Lead	affects expression	1
Silicon Dioxide	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases expression	1

Clinical trials (associated diseases)

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