PNMA6E

Summary

PNMA6E (PNMA family member 6E, HGNC:50767) is a protein-coding gene on chromosome Xq28, encoding Paraneoplastic antigen Ma6E (A0A0J9YXQ4).

At a glance

• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001367770

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:50767
Approved symbol	PNMA6E
Name	PNMA family member 6E
Location	Xq28
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000214897
Ensembl biotype	protein_coding
Entrez	649238

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000445091, ENST00000633844

RefSeq mRNA: 3 — MANE Select: NM_001367770 NM_001351293, NM_001351294, NM_001367770

CCDS: CCDS87793, CCDS94694

Canonical transcript exons

ENST00000445091 — 2 exons

Exon	Start	End
ENSE00001675703	153395639	153398920
ENSE00003780347	153401244	153401350

Expression profiles

Bgee: expression breadth broad, 21 present calls, max score 75.64.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0478 / max 34.4161, expressed in 6 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200865	0.0256	5
200866	0.0221	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	75.64	gold quality
left testis	UBERON:0004533	73.37	gold quality
testis	UBERON:0000473	73.30	gold quality
left ovary	UBERON:0002119	55.30	gold quality
ovary	UBERON:0000992	54.49	gold quality
right ovary	UBERON:0002118	51.65	gold quality
left uterine tube	UBERON:0001303	49.86	gold quality
colonic epithelium	UBERON:0000397	48.52	silver quality
apex of heart	UBERON:0002098	43.89	silver quality
fallopian tube	UBERON:0003889	43.29	gold quality
sural nerve	UBERON:0015488	43.21	gold quality
placenta	UBERON:0001987	42.19	silver quality
bone marrow cell	CL:0002092	41.00	gold quality
bone marrow	UBERON:0002371	40.95	gold quality
right uterine tube	UBERON:0001302	40.94	silver quality
left adrenal gland cortex	UBERON:0035825	40.16	gold quality
left adrenal gland	UBERON:0001234	39.54	gold quality
right adrenal gland cortex	UBERON:0035827	38.42	silver quality
adrenal gland	UBERON:0002369	38.41	gold quality
pituitary gland	UBERON:0000007	36.90	gold quality
adenohypophysis	UBERON:0002196	36.65	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
right coronary artery	UBERON:0001625	34.94	gold quality
skeletal muscle tissue	UBERON:0001134	34.80	gold quality
prefrontal cortex	UBERON:0000451	33.37	gold quality
muscle tissue	UBERON:0002385	33.20	gold quality
monocyte	CL:0000576	33.00	gold quality
prostate gland	UBERON:0002367	32.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.48

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pnma6e	ENSMUSG00000096966
mus_musculus	Gm45015	ENSMUSG00000109368
rattus_norvegicus	Pnma6e	ENSRNOG00000070467

Paralogs (13): MOAP1 (ENSG00000165943), ZCCHC18 (ENSG00000166707), CCDC8 (ENSG00000169515), ZCCHC12 (ENSG00000174460), PNMA1 (ENSG00000176903), PNMA8A (ENSG00000182013), PNMA3 (ENSG00000183837), PNMA5 (ENSG00000198883), PNMA8B (ENSG00000204851), PNMA6F (ENSG00000225110), PNMA6A (ENSG00000235961), PNMA2 (ENSG00000240694), PNMA8C (ENSG00000277531)

Protein

Protein identifiers

Paraneoplastic antigen Ma6E — A0A0J9YXQ4 (reviewed: A0A0J9YXQ4)

All UniProt accessions (2): A0A0J9YXH5, A0A0J9YXQ4

RefSeq proteins (3): NP_001338222, NP_001338223, NP_001354699* (*=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 5, region of interest 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A0J9YXQ4-F1	56.18	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): chrXq28, ZNF547_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

590 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PNMA6E	PNMA8B	Q9ULN7	596
PNMA6E	CT47A11	Q5JQC4	479
PNMA6E	CCDC8	Q9H0W5	397
PNMA6E	ERF	P50548	370
PNMA6E	KRTAP2-1	Q9BYU5	370
PNMA6E	CHCT1	Q86WR6	368
PNMA6E	DEFB123	Q8N688	365
PNMA6E	KBTBD12	Q3ZCT8	350
PNMA6E	KRTAP2-2	Q9BYT5	348
PNMA6E	CSKMT	A8MUP2	320
PNMA6E	PNMA8C	A0A1B0GUJ8	308
PNMA6E	SAXO2	Q658L1	305
PNMA6E	UMPS	P11172	303
PNMA6E	ARHGEF33	A8MVX0	300
PNMA6E	ACSM4	P0C7M7	281

IntAct

2 interactions, top by confidence:

A	B	Type	Score
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

404 predictions. Top by Δscore:

Variant	Effect	Δscore
X:153398641:G:C	donor_gain	1.0000
X:153401240:TCA:T	donor_loss	1.0000
X:153401242:A:AC	donor_gain	1.0000
X:153401242:ACT:A	donor_loss	1.0000
X:153401243:C:CC	donor_gain	1.0000
X:153401243:CTTT:C	donor_gain	1.0000
X:153398740:T:TA	donor_gain	0.9900
X:153398917:CAGC:C	acceptor_gain	0.9900
X:153398921:C:CC	acceptor_gain	0.9900
X:153398922:T:G	acceptor_loss	0.9900
X:153401170:T:TA	donor_gain	0.9900
X:153401238:ACT:A	donor_loss	0.9900
X:153401242:ACTTT:A	donor_gain	0.9900
X:153401243:CT:C	donor_gain	0.9900
X:153401243:CTT:C	donor_gain	0.9900
X:153401243:CTTTC:C	donor_gain	0.9900
X:153401246:T:A	donor_gain	0.9900
X:153398640:A:AC	donor_gain	0.9800
X:153398640:AG:A	donor_gain	0.9800
X:153398751:ATGTT:A	donor_gain	0.9800
X:153401239:CTCA:C	donor_gain	0.9800
X:153398647:TC:T	donor_gain	0.9700
X:153398648:CC:C	donor_gain	0.9700
X:153398709:G:A	donor_gain	0.9700
X:153398927:G:GC	acceptor_gain	0.9700
X:153401183:T:TA	donor_gain	0.9700
X:153398918:AGC:A	acceptor_gain	0.9600
X:153398927:G:C	acceptor_gain	0.9600
X:153398916:ACAGC:A	acceptor_gain	0.9500
X:153398917:CAGCC:C	acceptor_gain	0.9500

AlphaMissense

4102 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:153398643:G:C	F69L	0.975
X:153398643:G:T	F69L	0.975
X:153398645:A:G	F69L	0.975
X:153397575:G:C	F425L	0.974
X:153397575:G:T	F425L	0.974
X:153397577:A:G	F425L	0.974
X:153398745:G:C	F35L	0.967
X:153398745:G:T	F35L	0.967
X:153398747:A:G	F35L	0.967
X:153397656:A:C	F398L	0.963
X:153397656:A:T	F398L	0.963
X:153397658:A:G	F398L	0.963
X:153397617:G:C	F411L	0.962
X:153397617:G:T	F411L	0.962
X:153397619:A:G	F411L	0.962
X:153397407:G:C	F481L	0.960
X:153397407:G:T	F481L	0.960
X:153397409:A:G	F481L	0.960
X:153398746:A:G	F35S	0.956
X:153398585:A:G	W89R	0.955
X:153398585:A:T	W89R	0.955
X:153397561:T:A	E430V	0.953
X:153398773:A:G	I26T	0.946
X:153397878:A:C	F324L	0.943
X:153397878:A:T	F324L	0.943
X:153397880:A:G	F324L	0.943
X:153398782:A:G	I23T	0.943
X:153397762:A:G	L363P	0.941
X:153398583:C:A	W89C	0.940
X:153398583:C:G	W89C	0.940

dbSNP variants (sampled 300 via entrez): RS1000193816 (X:153411401 C>T), RS1000363661 (X:153402026 T>C), RS1000394886 (X:153402408 T>C), RS1000577523 (X:153396539 T>C), RS1000906407 (X:153396428 C>T), RS1001575798 (X:153403250 T>A), RS1001732311 (X:153396688 G>A), RS1001836334 (X:153411921 G>A,C,T), RS1002419299 (X:153409126 C>G,T), RS1002880349 (X:153409280 C>T), RS1003104422 (X:153413610 T>A,C), RS1004581552 (X:153401812 T>A,G), RS1004638100 (X:153396267 G>T), RS1004951021 (X:153401620 C>T), RS1005173782 (X:153405434 G>T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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