LYRM9

Summary

LYRM9 (LYR motif containing 9, HGNC:27314) is a protein-coding gene on chromosome 17q11.2, encoding LYR motif-containing protein 9 (A8MSI8).

Located in mitochondrion.

Source: NCBI Gene 201229 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 19 total
• MANE Select transcript: NM_001076680

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27314
Approved symbol	LYRM9
Name	LYR motif containing 9
Location	17q11.2
Locus type	gene with protein product
Status	Approved
Aliases	HSD24
Ensembl gene	ENSG00000232859
Ensembl biotype	protein_coding
Entrez	201229

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 25 protein_coding, 1 retained_intron

ENST00000379102, ENST00000379103, ENST00000460380, ENST00000503642, ENST00000508816, ENST00000508862, ENST00000582343, ENST00000860754, ENST00000860755, ENST00000860756, ENST00000860757, ENST00000860758, ENST00000860759, ENST00000860760, ENST00000860761, ENST00000860762, ENST00000860763, ENST00000860764, ENST00000860765, ENST00000860766, ENST00000922752, ENST00000922753, ENST00000971196, ENST00000971197, ENST00000971198, ENST00000971199

RefSeq mRNA: 1 — MANE Select: NM_001076680 NM_001076680

CCDS: CCDS45631

Canonical transcript exons

ENST00000379102 — 4 exons

Exon	Start	End
ENSE00002021487	27878358	27879490
ENSE00003567677	27882569	27882712
ENSE00003575746	27880274	27880366
ENSE00003902501	27893317	27893365

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 94.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5860 / max 88.8608, expressed in 1623 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164968	6.5860	1623

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
nucleus accumbens	UBERON:0001882	94.94	gold quality
prefrontal cortex	UBERON:0000451	94.25	gold quality
cingulate cortex	UBERON:0003027	94.11	gold quality
anterior cingulate cortex	UBERON:0009835	94.08	gold quality
amygdala	UBERON:0001876	93.91	gold quality
right frontal lobe	UBERON:0002810	93.57	gold quality
right adrenal gland cortex	UBERON:0035827	93.13	gold quality
Brodmann (1909) area 9	UBERON:0013540	93.12	gold quality
right adrenal gland	UBERON:0001233	92.84	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	92.61	gold quality
caudate nucleus	UBERON:0001873	92.54	gold quality
left adrenal gland	UBERON:0001234	92.51	gold quality
putamen	UBERON:0001874	92.46	gold quality
left adrenal gland cortex	UBERON:0035825	92.27	gold quality
frontal cortex	UBERON:0001870	92.04	gold quality
adrenal cortex	UBERON:0001235	91.88	gold quality
tibial nerve	UBERON:0001323	91.86	gold quality
neocortex	UBERON:0001950	91.75	gold quality
hypothalamus	UBERON:0001898	91.58	gold quality
right uterine tube	UBERON:0001302	91.05	gold quality
telencephalon	UBERON:0001893	91.02	gold quality
forebrain	UBERON:0001890	90.83	gold quality
frontal pole	UBERON:0002795	90.81	gold quality
adrenal gland	UBERON:0002369	90.78	gold quality
cerebral cortex	UBERON:0000956	90.77	gold quality
Brodmann (1909) area 10	UBERON:0013541	90.40	gold quality
Ammon’s horn	UBERON:0001954	90.39	gold quality
temporal lobe	UBERON:0001871	90.12	gold quality
left lobe of thyroid gland	UBERON:0001120	90.10	gold quality
adenohypophysis	UBERON:0002196	89.93	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

80 targeting LYRM9, 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-3925-3P	100.00	69.95	1237
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-10527-5P	99.91	72.28	3754

Literature-anchored findings (GeneRIF, showing 1)

• 3 SNPs associated with the fraction of exhaled nitric oxide in childhood asthma are rs3751972 in LYRM9; rs944722 in NOS2; and rs8069176 near GSDMB; all at 17q12-q21. (PMID:24315451)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lyrm9	ENSDARG00000075528
mus_musculus	Lyrm9	ENSMUSG00000072640
rattus_norvegicus	Lyrm9	ENSRNOG00000037204

Protein

Protein identifiers

LYR motif-containing protein 9 — A8MSI8 (reviewed: A8MSI8)

All UniProt accessions (4): A8MSI8, D6RAR2, D6RFL2, J3QLB4

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the complex I LYR family. LYRM9 subfamily.

RefSeq proteins (1): NP_001070148* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008011	Complex1_LYR_dom	Domain
IPR045291	Complex1_LYR_LYRM9	Domain
IPR052151	Complex_I_LYR	Family

Pfam: PF05347

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MSI8-F1	91.62	0.85

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 96 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, chr17q11, BROWNE_HCMV_INFECTION_48HR_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, OSMAN_BLADDER_CANCER_DN, PARENT_MTOR_SIGNALING_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP, KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP, KIM_ALL_DISORDERS_CALB1_CORR_UP, VERHAAK_GLIOBLASTOMA_NEURAL, PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP, KRIEG_KDM3A_TARGETS_NOT_HYPOXIA

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

412 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYRM9	LYRM2	Q9NU23	761
LYRM9	LYRM1	O43325	741
LYRM9	ETFRF1	Q6IPR1	703
LYRM9	LYRM7	Q5U5X0	641
LYRM9	NDUFAB1	O14561	606
LYRM9	FMC1	Q96HJ9	601
LYRM9	LYRM4	Q9HD34	596
LYRM9	SDHAF1	A6NFY7	594
LYRM9	NDUFB9	Q9Y6M9	542
LYRM9	NDUFA6	P56556	513
LYRM9	SDHAF3	Q9NRP4	509
LYRM9	OXLD1	Q5BKU9	464
LYRM9	TMEM242	Q9NWH2	453
LYRM9	MBLAC2	Q68D91	450
LYRM9	PIGBOS1	A0A0B4J2F0	443

IntAct

0 interactions, top by confidence:

BioGRID (1): LYRM9 (Affinity Capture-RNA)

ESM2 similar proteins: A3KNJ8, A3LNG8, A5D7J1, A5DH70, A5DY61, A7S1A4, A8MSI8, A9SNJ1, A9UMQ3, B2RYU8, B2RZD7, B3DFV0, B4F6X2, B5FXA0, B5FYC7, B5FZA8, B5X5U9, B5XCZ6, B6NK32, B8JLQ0, B9WD12, C4R7H7, C4Y4R9, C5DEI4, C5DR94, C9SBR9, D1Z4E1, L0R8F8, O43325, O60068, P42114, P82116, Q0UIG9, Q0VCG0, Q0VCR0, Q3UN90, Q503U1, Q5A7N3, Q6BQH4, Q6CTI7

Diamond homologs: A5D7J1, A8MSI8, B2RZD7, B3DFV0, B4F6X2, B6NK32, Q3UN90

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1776 predictions. Top by Δscore:

Variant	Effect	Δscore
17:27879939:C:A	donor_gain	1.0000
17:27880272:A:AC	donor_gain	1.0000
17:27880273:C:CC	donor_gain	1.0000
17:27880362:AAACT:A	acceptor_gain	1.0000
17:27880363:AACT:A	acceptor_gain	1.0000
17:27880365:CT:C	acceptor_gain	1.0000
17:27880365:CTCTG:C	acceptor_loss	1.0000
17:27880366:TCTGC:T	acceptor_loss	1.0000
17:27880367:C:CC	acceptor_gain	1.0000
17:27879938:T:TA	donor_gain	0.9900
17:27880267:CACCT:C	donor_loss	0.9900
17:27880268:ACCT:A	donor_loss	0.9900
17:27880270:CT:C	donor_loss	0.9900
17:27880270:CTAC:C	donor_loss	0.9900
17:27880271:TA:T	donor_loss	0.9900
17:27880272:AC:A	donor_loss	0.9900
17:27880272:ACT:A	donor_loss	0.9900
17:27880273:C:CG	donor_loss	0.9900
17:27880273:CT:C	donor_gain	0.9900
17:27880364:ACT:A	acceptor_gain	0.9900
17:27880365:CTC:C	acceptor_gain	0.9900
17:27880366:TCT:T	acceptor_gain	0.9900
17:27880368:T:A	acceptor_loss	0.9900
17:27880373:G:C	acceptor_gain	0.9900
17:27880375:T:C	acceptor_gain	0.9900
17:27880694:T:TA	donor_gain	0.9900
17:27880695:C:A	donor_gain	0.9900
17:27880705:T:TA	donor_gain	0.9900
17:27893131:G:C	donor_gain	0.9900
17:27879352:C:A	donor_gain	0.9800

AlphaMissense

507 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:27880294:C:G	A67P	0.995
17:27880306:C:G	A63P	0.995
17:27882576:A:T	V40D	0.981
17:27880361:A:C	F44L	0.980
17:27880361:A:T	F44L	0.980
17:27880363:A:G	F44L	0.980
17:27880297:C:G	D66H	0.978
17:27880305:G:T	A63D	0.976
17:27882636:A:G	L20S	0.975
17:27880296:T:G	D66A	0.974
17:27880354:G:C	H47D	0.974
17:27880286:C:A	W69C	0.973
17:27880286:C:G	W69C	0.973
17:27880293:G:T	A67D	0.972
17:27880288:A:G	W69R	0.971
17:27880288:A:T	W69R	0.971
17:27880295:A:C	D66E	0.970
17:27880295:A:T	D66E	0.970
17:27880296:T:A	D66V	0.969
17:27882648:A:G	L16P	0.969
17:27880352:A:C	H47Q	0.967
17:27880352:A:T	H47Q	0.967
17:27880296:T:C	D66G	0.964
17:27882646:A:C	Y17D	0.964
17:27882648:A:T	L16H	0.963
17:27880317:A:G	I59T	0.962
17:27880362:A:G	F44S	0.962
17:27882615:A:G	L27P	0.962
17:27880364:A:C	S43R	0.957
17:27880364:A:T	S43R	0.957

dbSNP variants (sampled 300 via entrez): RS1000209203 (17:27893882 A>C), RS1000915502 (17:27892996 T>TGA), RS1001070737 (17:27886291 A>G), RS1001167294 (17:27881084 A>G,T), RS1001537660 (17:27890585 G>T), RS1002049875 (17:27889748 A>C), RS1002059484 (17:27882385 C>A), RS1002116078 (17:27883946 G>A), RS1002204034 (17:27891910 C>T), RS1002246169 (17:27887270 C>T), RS1002318360 (17:27887663 T>C), RS1002525834 (17:27895243 A>G), RS1002583298 (17:27888816 A>C), RS1002804273 (17:27882361 G>GCA), RS1003141487 (17:27882098 ATACAT>A)

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

2 associations (top):

Study	Trait	p-value
GCST002304_1	Fractional exhaled nitric oxide (childhood)	2.000000e-10
GCST002304_18	Fractional exhaled nitric oxide (childhood)	7.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005536	nitric oxide exhalation measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	increases expression	3
Valproic Acid	affects cotreatment, decreases expression	3
Silicon Dioxide	decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
afuresertib	increases expression	1
methylmercuric chloride	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	affects expression	1
perfluorooctanoic acid	increases expression	1
dinophysistoxin 1	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Imatinib Mesylate	affects response to substance	1
Resveratrol	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Catechin	affects cotreatment, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dimethyl Sulfoxide	affects expression	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1
Niclosamide	increases expression	1
Smoke	decreases expression	1
Triiodothyronine	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_C0QP	HEK Flp-In T-REx-293-LYRM9-KO	Transformed cell line	Female

Clinical trials (associated diseases)

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