PNMA6A

Summary

PNMA6A (PNMA family member 6A, HGNC:28248) is a protein-coding gene on chromosome Xq28, encoding Paraneoplastic antigen-like protein 6A (P0CW24).

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_032882

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28248
Approved symbol	PNMA6A
Name	PNMA family member 6A
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	MGC15827
Ensembl gene	ENSG00000235961
Ensembl biotype	protein_coding
OMIM	300917
Entrez	84968

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000421798

RefSeq mRNA: 1 — MANE Select: NM_032882 NM_032882

CCDS: CCDS14719

Canonical transcript exons

ENST00000421798 — 2 exons

Exon	Start	End
ENSE00001718954	153072935	153075019
ENSE00003162721	153072454	153072606

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 92.66.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	92.66	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.30	gold quality
right frontal lobe	UBERON:0002810	89.97	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.39	gold quality
anterior cingulate cortex	UBERON:0009835	88.61	gold quality
Brodmann (1909) area 23	UBERON:0013554	88.59	gold quality
superior frontal gyrus	UBERON:0002661	88.57	gold quality
primary visual cortex	UBERON:0002436	88.21	gold quality
middle temporal gyrus	UBERON:0002771	88.04	gold quality
kidney epithelium	UBERON:0004819	87.82	gold quality
occipital lobe	UBERON:0002021	87.63	gold quality
cerebellar vermis	UBERON:0004720	87.36	gold quality
parietal lobe	UBERON:0001872	87.30	gold quality
hypothalamus	UBERON:0001898	87.26	gold quality
postcentral gyrus	UBERON:0002581	87.19	gold quality
neocortex	UBERON:0001950	86.77	gold quality
frontal cortex	UBERON:0001870	86.57	gold quality
cerebral cortex	UBERON:0000956	86.42	gold quality
lateral nuclear group of thalamus	UBERON:0002736	84.82	gold quality
temporal lobe	UBERON:0001871	84.48	gold quality
entorhinal cortex	UBERON:0002728	84.41	gold quality
amygdala	UBERON:0001876	84.36	gold quality
forebrain	UBERON:0001890	84.19	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.10	gold quality
brain	UBERON:0000955	83.94	gold quality
prefrontal cortex	UBERON:0000451	83.55	gold quality
cerebellar hemisphere	UBERON:0002245	83.04	gold quality
cerebellar cortex	UBERON:0002129	83.03	gold quality
cerebellum	UBERON:0002037	82.96	gold quality
substantia nigra pars compacta	UBERON:0001965	82.68	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-99795	no	5.22
E-ANND-3	no	2.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting PNMA6A, 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-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-7109-5P	99.18	66.13	1057
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-4700-5P	98.63	67.43	1915
HSA-MIR-6887-5P	98.56	68.49	1295
HSA-MIR-6795-5P	98.52	68.51	1277
HSA-MIR-6882-3P	98.23	67.01	1119
HSA-MIR-296-5P	97.61	64.02	851
HSA-MIR-4797-3P	97.48	67.14	989
HSA-MIR-181D-3P	96.23	63.96	81

Cross-species orthologs

0 orthologs

Paralogs (13): MOAP1 (ENSG00000165943), ZCCHC18 (ENSG00000166707), CCDC8 (ENSG00000169515), ZCCHC12 (ENSG00000174460), PNMA1 (ENSG00000176903), PNMA8A (ENSG00000182013), PNMA3 (ENSG00000183837), PNMA5 (ENSG00000198883), PNMA8B (ENSG00000204851), PNMA6E (ENSG00000214897), PNMA6F (ENSG00000225110), PNMA2 (ENSG00000240694), PNMA8C (ENSG00000277531)

Protein

Protein identifiers

Paraneoplastic antigen-like protein 6A — P0CW24 (reviewed: P0CW24)

All UniProt accessions (1): P0CW24

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in the brain.

Similarity. Belongs to the PNMA family.

RefSeq proteins (1): NP_116271* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF14893, PF20846

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CW24-F1	75.53	0.40

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): ATF_B, CREBP1_Q2, CREB_Q4, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, E4F1_Q6, ATF3_Q6, CREB_Q2_01, ATF4_Q2, ATF_01, CREBP1CJUN_01, CREB_01, TGACGTCA_ATF3_Q6, CREB_Q2, YGCANTGCR_UNKNOWN, chrXq28

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

574 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PNMA6A	NPIPA7	E9PJI5	541
PNMA6A	PRDX3	P30048	506
PNMA6A	RTL6	Q6ICC9	506
PNMA6A	PWWP4	A0A494C071	480
PNMA6A	RMP24	Q32NC0	479
PNMA6A	HLA-DRB5	Q30154	449
PNMA6A	CDR2L	Q86X02	445
PNMA6A	RTL8B	Q17RB0	431
PNMA6A	TCP11X2	Q5H9J9	399
PNMA6A	TFF3	Q07654	371
PNMA6A	ANKRD34A	Q69YU3	370
PNMA6A	TIGD1	Q96MW7	369
PNMA6A	CREG2	Q8IUH2	348
PNMA6A	LDOC1	O95751	348
PNMA6A	MANEAL	Q5VSG8	348

IntAct

29 interactions, top by confidence:

A	B	Type	Score
PNMA6A	PNMA1	psi-mi:“MI:0915”(physical association)	0.870
PNMA1	PNMA6A	psi-mi:“MI:0915”(physical association)	0.870
CRX	PNMA6A	psi-mi:“MI:0915”(physical association)	0.560
	PNMA6A	psi-mi:“MI:0915”(physical association)	0.560
PNMA6A	DNAAF19	psi-mi:“MI:0915”(physical association)	0.560
PNMA6A	ARMC7	psi-mi:“MI:0915”(physical association)	0.560
DAP3	PNMA6A	psi-mi:“MI:0914”(association)	0.530
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
PNMA2	TARS3	psi-mi:“MI:0914”(association)	0.350
KIR2DL4	GPR89A	psi-mi:“MI:0914”(association)	0.350
PNMA6A	ZFTRAF1	psi-mi:“MI:0914”(association)	0.350
PNMA6A	SLC27A2	psi-mi:“MI:0914”(association)	0.350
PNMA6A	PNMA6A	psi-mi:“MI:0914”(association)	0.350
PNMA1	VWA8	psi-mi:“MI:0914”(association)	0.350
CRX	PNMA6A	psi-mi:“MI:0915”(physical association)	0.000
PNMA6A	CRX	psi-mi:“MI:0915”(physical association)	0.000
PNMA6A	PNMA1	psi-mi:“MI:0915”(physical association)	0.000
PNMA6A		psi-mi:“MI:0915”(physical association)	0.000
DNAAF19	PNMA6A	psi-mi:“MI:0915”(physical association)	0.000
ARMC7	PNMA6A	psi-mi:“MI:0915”(physical association)	0.000

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, 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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

298 predictions. Top by Δscore:

Variant	Effect	Δscore
X:153072603:AAAGG:A	donor_loss	1.0000
X:153072604:AAGGT:A	donor_loss	1.0000
X:153072605:AGGTA:A	donor_loss	1.0000
X:153072605:C:CT	donor_loss	1.0000
X:153072606:ACCT:A	donor_loss	1.0000
X:153072607:GTATC:G	donor_loss	1.0000
X:153072607:TACCT:T	donor_loss	1.0000
X:153072608:ATACC:A	donor_loss	1.0000
X:153072608:T:A	donor_loss	1.0000
X:153072609:GATAC:G	donor_loss	1.0000
X:153072610:TGATA:T	donor_loss	1.0000
X:153072583:T:TA	donor_gain	0.9900
X:153072584:G:GT	donor_gain	0.9900
X:153073974:G:GT	donor_gain	0.9900
X:153073978:C:G	donor_gain	0.9900
X:153073992:G:GT	donor_gain	0.9900
X:153073992:G:T	donor_gain	0.9900
X:153073276:G:GT	donor_gain	0.9800
X:153072936:CAGC:C	acceptor_gain	0.9700
X:153073275:T:TA	donor_gain	0.9700
X:153073276:G:T	donor_gain	0.9700
X:153073996:TCTCC:T	donor_gain	0.9700
X:153074086:G:GT	donor_gain	0.9700
X:153072931:T:A	acceptor_loss	0.9500
X:153072932:C:CC	acceptor_gain	0.9500
X:153072932:CT:C	acceptor_loss	0.9500
X:153072933:CCT:C	acceptor_loss	0.9500
X:153072934:GCCTG:G	acceptor_loss	0.9500
X:153073274:C:A	donor_gain	0.9500
X:153072607:G:GG	donor_gain	0.9400

AlphaMissense

2564 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:153073837:T:C	F259L	0.980
X:153073839:C:A	F259L	0.980
X:153073839:C:G	F259L	0.980
X:153073756:T:C	F232L	0.973
X:153073758:T:A	F232L	0.973
X:153073758:T:G	F232L	0.973
X:153073534:T:C	F158L	0.971
X:153073536:T:A	F158L	0.971
X:153073536:T:G	F158L	0.971
X:153073228:T:C	F56L	0.952
X:153073230:T:A	F56L	0.952
X:153073230:T:G	F56L	0.952
X:153074005:T:C	F315L	0.949
X:153074007:C:A	F315L	0.949
X:153074007:C:G	F315L	0.949
X:153073262:T:A	V67D	0.924
X:153073130:T:C	I23T	0.922
X:153074027:T:A	V322D	0.915
X:153073573:T:C	F171L	0.909
X:153073575:T:A	F171L	0.909
X:153073575:T:G	F171L	0.909
X:153074006:T:C	F315S	0.909
X:153073130:T:A	I23N	0.901
X:153073853:A:T	E264V	0.901
X:153073130:T:G	I23S	0.900
X:153074035:T:C	S325P	0.898
X:153073139:T:C	I26T	0.897
X:153073535:T:C	F158S	0.892
X:153073838:T:G	F259C	0.886
X:153073582:T:A	W174R	0.884

dbSNP variants (sampled 300 via entrez): RS1000176589 (X:153075347 C>T), RS1006487434 (X:153074514 C>T), RS1006622743 (X:153074707 G>A), RS1011150585 (X:153074752 G>A), RS1011621893 (X:153075138 G>C), RS1012395609 (X:153075422 C>A,T), RS1012426781 (X:153075181 G>A,C), RS1017878668 (X:153074712 G>T), RS1017908117 (X:153074517 G>T), RS1019968779 (X:153075139 G>A), RS1022459885 (X:153074551 C>G), RS1023683021 (X:153075188 C>A,T), RS1023822062 (X:153075431 C>T), RS1026061377 (X:153075464 C>G), RS1029789731 (X:153074492 T>C,G)

Disease associations

OMIM: gene MIM:300917 | 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

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	1
jinfukang	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Allergens	increases expression, decreases expression, decreases reaction, increases abundance	1
Vehicle Emissions	decreases reaction, increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Lead	affects expression	1
Methotrexate	increases expression	1
Quartz	increases expression	1
Quercetin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases methylation	1
Antirheumatic Agents	increases expression	1
Acrylamide	decreases expression	1
Particulate Matter	increases expression, decreases reaction, increases abundance	1

Clinical trials (associated diseases)

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