LYRM2

Summary

LYRM2 (LYR motif containing 2, HGNC:25229) is a protein-coding gene on chromosome 6q15, encoding LYR motif-containing protein 2 (Q9NU23). Involved in efficient integration of the N-module into mitochondrial respiratory chain complex I.

Involved in mitochondrial respiratory chain complex I assembly. Located in mitochondrion.

Source: NCBI Gene 57226 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_020466

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25229
Approved symbol	LYRM2
Name	LYR motif containing 2
Location	6q15
Locus type	gene with protein product
Status	Approved
Aliases	DJ122O8.2
Ensembl gene	ENSG00000083099
Ensembl biotype	protein_coding
Entrez	57226

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 protein_coding_CDS_not_defined, 5 protein_coding, 1 nonsense_mediated_decay

ENST00000412237, ENST00000517396, ENST00000520318, ENST00000520441, ENST00000520897, ENST00000521961, ENST00000523075, ENST00000523377, ENST00000523793, ENST00000524153, ENST00000626778, ENST00000943210

RefSeq mRNA: 1 — MANE Select: NM_020466 NM_020466

CCDS: CCDS5023

Canonical transcript exons

ENST00000523377 — 3 exons

Exon	Start	End
ENSE00002095650	89632224	89637353
ENSE00002122972	89638672	89638747
ENSE00003593686	89637742	89637882

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 95.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.8938 / max 444.9620, expressed in 1792 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
74701	18.6949	1783
74700	3.1989	1474

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	95.56	gold quality
islet of Langerhans	UBERON:0000006	93.87	gold quality
adrenal tissue	UBERON:0018303	93.50	gold quality
rectum	UBERON:0001052	92.72	gold quality
tendon of biceps brachii	UBERON:0008188	91.47	gold quality
ventricular zone	UBERON:0003053	91.18	gold quality
monocyte	CL:0000576	91.16	gold quality
mononuclear cell	CL:0000842	90.99	gold quality
ganglionic eminence	UBERON:0004023	90.87	gold quality
decidua	UBERON:0002450	90.53	gold quality
leukocyte	CL:0000738	90.44	gold quality
gall bladder	UBERON:0002110	89.88	gold quality
gastrocnemius	UBERON:0001388	89.73	gold quality
muscle of leg	UBERON:0001383	89.57	gold quality
adrenal gland	UBERON:0002369	89.03	gold quality
medial globus pallidus	UBERON:0002477	89.02	gold quality
bronchial epithelial cell	CL:0002328	88.91	gold quality
right adrenal gland cortex	UBERON:0035827	88.87	gold quality
right adrenal gland	UBERON:0001233	88.79	gold quality
left adrenal gland	UBERON:0001234	88.77	gold quality
pigmented layer of retina	UBERON:0001782	88.73	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	88.37	gold quality
adrenal cortex	UBERON:0001235	88.34	gold quality
globus pallidus	UBERON:0001875	88.25	gold quality
mucosa of sigmoid colon	UBERON:0004993	88.23	gold quality
left adrenal gland cortex	UBERON:0035825	88.16	gold quality
corpus callosum	UBERON:0002336	88.12	gold quality
inferior vagus X ganglion	UBERON:0005363	88.04	gold quality
spinal cord	UBERON:0002240	87.97	gold quality
muscle organ	UBERON:0001630	87.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

142 targeting LYRM2, 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-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-30A-3P	99.87	69.74	2928

Literature-anchored findings (GeneRIF, showing 1)

• Authors identified a new Akt-S58phos-LYRM2-Complex I axis, which is responsible for the LYRM2-induced tumor growth and the activation of OXPHOS in colorectal cancer. (PMID:31004700)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lyrm2	ENSMUSG00000045854
rattus_norvegicus	Lyrm2	ENSRNOG00000043105

Protein

Protein identifiers

LYR motif-containing protein 2 — Q9NU23 (reviewed: Q9NU23)

All UniProt accessions (4): Q9NU23, E5RG38, E5RJK7, G3V136

UniProt curated annotations — full annotation on UniProt →

Function. Involved in efficient integration of the N-module into mitochondrial respiratory chain complex I.

Subcellular location. Mitochondrion.

Similarity. Belongs to the complex I LYR family.

RefSeq proteins (1): NP_065199* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008011	Complex1_LYR_dom	Domain
IPR045293	Complex1_LYR_LYRM2	Domain

Pfam: PF05347

UniProt features (5 total): sequence variant 3, transit peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NU23-F1	93.03	0.82

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-6799198	Complex I biogenesis
R-HSA-1428517	Aerobic respiration and respiratory electron transport
R-HSA-1430728	Metabolism
R-HSA-611105	Respiratory electron transport

MSigDB gene sets: 100 (showing top): chr6q15, LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY, WANG_LMO4_TARGETS_DN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, TIEN_INTESTINE_PROBIOTICS_24HR_UP, MODULE_207, IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP, NUYTTEN_EZH2_TARGETS_DN, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, MARTENS_TRETINOIN_RESPONSE_DN, GOBP_NADH_DEHYDROGENASE_COMPLEX_ASSEMBLY, RAO_BOUND_BY_SALL4_ISOFORM_B

GO Biological Process (1): mitochondrial respiratory chain complex I assembly (GO:0032981)

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

GO Cellular Component (1): mitochondrion (GO:0005739)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Respiratory electron transport	1
Metabolism	1
Aerobic respiration and respiratory electron transport	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
NADH dehydrogenase complex assembly	1
mitochondrial respiratory chain complex assembly	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

556 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYRM2	LYRM1	O43325	788
LYRM2	ETFRF1	Q6IPR1	782
LYRM2	LYRM9	A8MSI8	761
LYRM2	LYRM4	Q9HD34	687
LYRM2	SDHAF3	Q9NRP4	639
LYRM2	LYRM7	Q5U5X0	635
LYRM2	FMC1	Q96HJ9	580
LYRM2	NDUFB9	Q9Y6M9	520
LYRM2	SDHAF1	A6NFY7	510
LYRM2	WDR55	Q9H6Y2	497
LYRM2	NDUFAB1	O14561	472
LYRM2	NDUFA6	P56556	467
LYRM2	KYAT3	Q6YP21	462
LYRM2	PGAP2	Q9UHJ9	459
LYRM2	NFS1	Q9Y697	458

IntAct

17 interactions, top by confidence:

A	B	Type	Score
LYRM2	NDUFAB1	psi-mi:“MI:0914”(association)	0.730
YARS2	HSPD1	psi-mi:“MI:0914”(association)	0.710
FAM9B	LYRM2	psi-mi:“MI:0915”(physical association)	0.670
LYRM2	FAM9B	psi-mi:“MI:0915”(physical association)	0.670
MANBAL	S100A6	psi-mi:“MI:0914”(association)	0.530
YARS2	HNRNPK	psi-mi:“MI:0914”(association)	0.350

BioGRID (35): FAM9B (Two-hybrid), LYRM2 (Affinity Capture-MS), LYRM2 (Affinity Capture-MS), ECH1 (Affinity Capture-MS), NDUFAB1 (Affinity Capture-MS), POLDIP2 (Affinity Capture-MS), MRPL13 (Affinity Capture-MS), C1QBP (Affinity Capture-MS), PMPCB (Affinity Capture-MS), NDUFAB1 (Affinity Capture-MS), OXSM (Affinity Capture-MS), LYRM2 (Affinity Capture-MS), ACADS (Affinity Capture-MS), LYRM2 (Co-fractionation), LYRM2 (Co-fractionation)

ESM2 similar proteins: A5D7J1, A5PLG0, A6ZYX9, A7S1A4, A7S1H9, A8MSI8, A9SNJ1, B2GV91, B2RZD7, B3DFV0, B4F6X2, B5FZA8, B5X5U9, B5XD90, B5XFA7, B6NK32, B8JLQ0, G2TRP8, L0R8F8, O46098, O60068, P42114, P82116, Q04401, Q0VCG0, Q32LM5, Q3E785, Q3UN90, Q4SQJ2, Q503U1, Q54F42, Q54FN9, Q54HG5, Q59L89, Q5RES3, Q5RIM0, Q5XIY4, Q6BIY6, Q6CUY0, Q6DCS1

Diamond homologs: B2GV91, B3DLF3, B5XFA7, Q32LM5, Q5PQ90, Q5RES3, Q5RIM0, Q8R033, Q9NU23

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	3
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3246 predictions. Top by Δscore:

Variant	Effect	Δscore
6:89596015:G:GG	donor_gain	1.0000
6:89603016:T:TA	acceptor_gain	1.0000
6:89603020:A:AG	acceptor_gain	1.0000
6:89603021:C:G	acceptor_gain	1.0000
6:89603024:T:TA	acceptor_gain	1.0000
6:89603024:TGCA:T	acceptor_loss	1.0000
6:89603026:CA:C	acceptor_loss	1.0000
6:89603027:A:AG	acceptor_gain	1.0000
6:89603027:AG:A	acceptor_gain	1.0000
6:89603027:AGG:A	acceptor_gain	1.0000
6:89603027:AGGG:A	acceptor_gain	1.0000
6:89603027:AGGGG:A	acceptor_gain	1.0000
6:89603028:G:GT	acceptor_gain	1.0000
6:89603028:GG:G	acceptor_gain	1.0000
6:89603028:GGG:G	acceptor_gain	1.0000
6:89603028:GGGG:G	acceptor_gain	1.0000
6:89603028:GGGGG:G	acceptor_gain	1.0000
6:89603126:AGGTG:A	donor_loss	1.0000
6:89603127:GGTG:G	donor_loss	1.0000
6:89603128:G:GC	donor_loss	1.0000
6:89603128:G:GG	donor_gain	1.0000
6:89603129:T:A	donor_loss	1.0000
6:89623523:G:GT	donor_gain	1.0000
6:89623961:G:GT	donor_gain	1.0000
6:89623962:A:T	donor_gain	1.0000
6:89624533:TCTTA:T	acceptor_loss	1.0000
6:89624534:CTTA:C	acceptor_loss	1.0000
6:89624536:TAGGC:T	acceptor_loss	1.0000
6:89624537:A:AG	acceptor_gain	1.0000
6:89624537:AGGC:A	acceptor_loss	1.0000

AlphaMissense

570 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:89637326:C:G	G72R	0.979
6:89637880:G:C	F16L	0.978
6:89637880:G:T	F16L	0.978
6:89637882:A:G	F16L	0.978
6:89637313:A:G	L76P	0.977
6:89637325:C:T	G72D	0.977
6:89637770:A:G	F53S	0.976
6:89637769:G:C	F53L	0.973
6:89637769:G:T	F53L	0.973
6:89637771:A:G	F53L	0.973
6:89637794:A:G	L45P	0.969
6:89637783:C:G	A49P	0.960
6:89637304:A:G	L79S	0.955
6:89637852:A:C	Y26D	0.955
6:89637786:A:G	W48R	0.942
6:89637786:A:T	W48R	0.942
6:89637782:G:T	A49E	0.938
6:89637336:C:A	M68I	0.929
6:89637336:C:G	M68I	0.929
6:89637336:C:T	M68I	0.929
6:89637784:C:A	W48C	0.924
6:89637784:C:G	W48C	0.924
6:89637325:C:A	G72V	0.922
6:89637292:A:G	L83P	0.921
6:89637343:C:G	R66P	0.920
6:89637863:A:T	V22D	0.920
6:89637821:A:T	V36D	0.918
6:89637872:C:A	R19M	0.917
6:89637346:A:T	I65N	0.909
6:89637881:A:G	F16S	0.908

dbSNP variants (sampled 300 via entrez): RS1000033059 (6:89638524 A>G), RS1001279278 (6:89633281 A>G), RS1001331580 (6:89633605 A>G), RS1001579253 (6:89638913 T>C), RS1003618449 (6:89639745 T>C), RS1003764996 (6:89639422 T>G), RS1005205680 (6:89638865 G>A,T), RS1005236721 (6:89639331 C>T), RS1005630236 (6:89632029 GA>G), RS1005681281 (6:89632270 AAAAC>A,AAAACAAAC), RS1006279020 (6:89636536 G>A), RS1006807387 (6:89632612 A>G), RS1007661530 (6:89640438 G>A), RS1007832830 (6:89637111 T>C), RS1007959119 (6:89634265 G>C)

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

1 associations (top):

Study	Trait	p-value
GCST005194_75	Coronary artery disease	4.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	2
GSK-J4	decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Arsenic	decreases methylation	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Gasoline	affects cotreatment, decreases expression, increases abundance	1
Phenobarbital	affects expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, decreases expression, increases abundance	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Valproic Acid	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Aflatoxin M1	decreases expression	1
Antirheumatic Agents	decreases expression	1
Particulate Matter	decreases expression, increases abundance, affects cotreatment	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_SW17	HAP1 LYRM2 (-) 1	Cancer cell line	Male
CVCL_XQ25	HAP1 LYRM2 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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