MKRN2OS

Summary

MKRN2OS (MKRN2 opposite strand, HGNC:40375) is a protein-coding gene on chromosome 3p25.2, encoding MKRN2 opposite strand protein (H3BPM6).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 63 total
• MANE Select transcript: NM_001195279

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40375
Approved symbol	MKRN2OS
Name	MKRN2 opposite strand
Location	3p25.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000225526
Ensembl biotype	protein_coding
Entrez	100129480

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding_CDS_not_defined, 2 protein_coding, 1 nonsense_mediated_decay

ENST00000447550, ENST00000561645, ENST00000564146, ENST00000567514, ENST00000678164, ENST00000896064

RefSeq mRNA: 4 — MANE Select: NM_001195279 NM_001195279, NM_001378009, NM_001378010, NM_001378011

CCDS: CCDS58816

Canonical transcript exons

ENST00000564146 — 4 exons

Exon	Start	End
ENSE00002587189	12545247	12545499
ENSE00003516405	12541860	12542022
ENSE00003592261	12543180	12543229
ENSE00003639896	12539776	12540433

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 85.49.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0367 / max 13.1079, expressed in 15 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41128	0.0367	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellum	UBERON:0002037	85.49	gold quality
cerebellar cortex	UBERON:0002129	85.38	gold quality
cerebellar hemisphere	UBERON:0002245	85.37	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.80	gold quality
duodenum	UBERON:0002114	79.47	gold quality
mucosa of transverse colon	UBERON:0004991	78.50	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	77.17	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.55	silver quality
rectum	UBERON:0001052	75.33	gold quality
esophagus mucosa	UBERON:0002469	75.24	gold quality
lower esophagus mucosa	UBERON:0035834	75.19	gold quality
body of pancreas	UBERON:0001150	74.22	gold quality
saliva-secreting gland	UBERON:0001044	74.05	gold quality
minor salivary gland	UBERON:0001830	73.50	gold quality
hindlimb stylopod muscle	UBERON:0004252	73.29	gold quality
pancreas	UBERON:0001264	72.75	gold quality
islet of Langerhans	UBERON:0000006	72.12	gold quality
transverse colon	UBERON:0001157	70.95	gold quality
small intestine	UBERON:0002108	70.61	gold quality
small intestine Peyer’s patch	UBERON:0003454	70.59	gold quality
prefrontal cortex	UBERON:0000451	70.13	gold quality
apex of heart	UBERON:0002098	69.31	gold quality
frontal cortex	UBERON:0001870	69.29	gold quality
superior frontal gyrus	UBERON:0002661	69.18	gold quality
body of stomach	UBERON:0001161	69.15	gold quality
Brodmann (1909) area 9	UBERON:0013540	68.74	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	68.19	gold quality
esophagus	UBERON:0001043	68.14	gold quality
skin of leg	UBERON:0001511	68.05	gold quality
stomach	UBERON:0000945	68.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting MKRN2OS, 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-590-3P	99.96	74.34	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-5700	99.64	69.88	2280
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-140-3P	99.04	67.69	1324
HSA-MIR-5089-5P	98.45	66.06	1388
HSA-MIR-1278	97.75	67.55	628
HSA-MIR-3920	97.75	69.02	1168
HSA-MIR-552-3P	96.68	64.12	1026
HSA-MIR-4259	95.68	65.25	582

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mkrn2os.2	ENSDARG00000100728
mus_musculus	Mkrn2os	ENSMUSG00000068011
rattus_norvegicus	Mkrn2os	ENSRNOG00000070957

Protein

Protein identifiers

MKRN2 opposite strand protein — H3BPM6 (reviewed: H3BPM6)

Alternative names: MKRN2 antisense RNA 1, MKRN2 antisense gene protein 1

All UniProt accessions (2): H3BPM6, H3BSJ0

RefSeq proteins (4): NP_001182208, NP_001364938, NP_001364939, NP_001364940 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032016	MKRN2OS-like	Family
IPR053921	MKRN2OS-like_C	Domain
IPR053922	MKRN2OS-like_N	Domain

Pfam: PF16044, PF22795

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H3BPM6-F1	90.36	0.81

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, HMGA1_TARGET_GENES, LHX9_TARGET_GENES, ZFP3_TARGET_GENES, ZNF33A_TARGET_GENES, MIR1278, DESCARTES_MAIN_FETAL_CSH1_CSH2_POSITIVE_CELLS, CUX1_TARGET_GENES, MEF2C_TARGET_GENES, HE_LIM_SUN_FETAL_LUNG_C1_SMG_CELL, GENES_CORRELATED_WITH_RAB35_DELETION, chr3p25

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

46 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MKRN2OS	ANKMY1	Q9P2S6	621
MKRN2OS	MARF1	Q9Y4F3	479
MKRN2OS	DYRK3	O43781	400
MKRN2OS	UBR1	Q8IWV7	368
MKRN2OS	SNAPC2	Q13487	351
MKRN2OS	DDR1	Q08345	333
MKRN2OS	SNAPC4	Q5SXM2	308
MKRN2OS	UPP2	O95045	244
MKRN2OS	ACY1	Q03154	222
MKRN2OS	NAGA	P17050	208
MKRN2OS	UPP1	Q16831	205
MKRN2OS	RNGTT	O60942	201
MKRN2OS	RNF146	Q9NTX7	194
MKRN2OS	SLC28A2	O43868	189
MKRN2OS	AURKA	O14965	187

IntAct

0 interactions, top by confidence:

BioGRID (1): MKRN2OS (Affinity Capture-RNA)

ESM2 similar proteins: A4GT88, A7MBC2, A7YD35, F1Q7Z7, F1S5L4, H3BPM6, O15111, O42412, O88351, O95822, P09543, P13233, P16330, P24389, P27229, P27555, P49894, P49895, P49896, P49898, P49899, P97564, Q02556, Q0VCH3, Q1LYL8, Q32NQ7, Q5F259, Q5GJ77, Q5RFD0, Q5XUN4, Q60680, Q61153, Q61179, Q61586, Q62240, Q66HY8, Q6NVV7, Q6P996, Q6QN11, Q6QN13

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1629 predictions. Top by Δscore:

Variant	Effect	Δscore
3:12519048:A:G	acceptor_gain	1.0000
3:12519051:A:AG	acceptor_gain	1.0000
3:12519198:G:GG	donor_gain	1.0000
3:12529760:A:AG	acceptor_gain	1.0000
3:12529761:G:GG	acceptor_gain	1.0000
3:12529761:GTT:G	acceptor_gain	1.0000
3:12541855:TGTA:T	donor_loss	1.0000
3:12541856:GTACC:G	donor_loss	1.0000
3:12541857:TACCT:T	donor_loss	1.0000
3:12541858:A:AT	donor_loss	1.0000
3:12541859:CCTGT:C	donor_loss	1.0000
3:12542020:CCC:C	acceptor_gain	1.0000
3:12542021:CCC:C	acceptor_gain	1.0000
3:12543226:CTCT:C	acceptor_gain	1.0000
3:12557174:CAG:C	donor_loss	1.0000
3:12557177:G:GA	donor_loss	1.0000
3:12557178:T:A	donor_loss	1.0000
3:12519047:A:AG	acceptor_gain	0.9900
3:12519052:A:G	acceptor_gain	0.9900
3:12519054:TTTAG:T	acceptor_loss	0.9900
3:12519057:A:AG	acceptor_gain	0.9900
3:12519057:AG:A	acceptor_gain	0.9900
3:12519057:AGG:A	acceptor_loss	0.9900
3:12519058:G:GG	acceptor_gain	0.9900
3:12519058:GG:G	acceptor_gain	0.9900
3:12519058:GGA:G	acceptor_gain	0.9900
3:12519193:TTTAC:T	donor_gain	0.9900
3:12519195:TACG:T	donor_loss	0.9900
3:12519196:ACG:A	donor_loss	0.9900
3:12519197:CGTAA:C	donor_loss	0.9900

AlphaMissense

1475 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:12541912:A:G	W127R	0.995
3:12541912:A:T	W127R	0.995
3:12541970:C:A	W107C	0.995
3:12541970:C:G	W107C	0.995
3:12541972:A:G	W107R	0.995
3:12541972:A:T	W107R	0.995
3:12540335:A:G	F177S	0.992
3:12541910:C:A	W127C	0.992
3:12541910:C:G	W127C	0.992
3:12545280:A:G	F62S	0.990
3:12540388:G:C	F159L	0.989
3:12540388:G:T	F159L	0.989
3:12540390:A:G	F159L	0.989
3:12540334:A:C	F177L	0.988
3:12540334:A:T	F177L	0.988
3:12540336:A:G	F177L	0.988
3:12541961:G:C	S110R	0.988
3:12541961:G:T	S110R	0.988
3:12541963:T:G	S110R	0.988
3:12545252:A:C	F71L	0.988
3:12545252:A:T	F71L	0.988
3:12545254:A:G	F71L	0.988
3:12541873:A:G	W140R	0.987
3:12541873:A:T	W140R	0.987
3:12540389:A:G	F159S	0.984
3:12541971:C:G	W107S	0.984
3:12543194:A:T	I85K	0.984
3:12541911:C:G	W127S	0.982
3:12543200:A:T	V83D	0.981
3:12543194:A:C	I85R	0.980

dbSNP variants (sampled 300 via entrez): RS1000022363 (3:12548821 C>A,T), RS1000090405 (3:12549036 G>C), RS1000129221 (3:12556747 A>G,T), RS1000143842 (3:12557990 C>G), RS1000368371 (3:12561181 A>G), RS1000574675 (3:12544594 A>G), RS1000739190 (3:12539385 T>C), RS1000771687 (3:12559886 A>G,T), RS1000902823 (3:12543912 A>C), RS1001116200 (3:12554963 C>A,T), RS1001214351 (3:12549573 G>A,C,T), RS1001251906 (3:12555462 T>C), RS1001272821 (3:12543774 C>T), RS1001402846 (3:12544242 G>A), RS1001407755 (3:12548739 A>G)

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
GCST90020025_1924	Waist-to-hip ratio adjusted for BMI	2.000000e-10
GCST90020026_186	Hip index	2.000000e-12
GCST90020027_154	Waist-hip index	2.000000e-11
GCST90020028_705	Hip circumference adjusted for BMI	1.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008039	BMI-adjusted hip circumference

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
Estradiol	affects cotreatment, decreases expression	2
licochalcone B	decreases expression	1
Cadmium Chloride	increases expression	1
Particulate Matter	increases expression	1
Magnetite Nanoparticles	decreases expression	1

Clinical trials (associated diseases)

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