MIMS1

Summary

MIMS1 (mitochondrial inner membrane scaffold 1, HGNC:28346) is a protein-coding gene on chromosome 18p11.21, encoding Protein FAM210A (Q96ND0). May play a role in the structure and strength of both muscle and bone. It is a selective cancer dependency (DepMap: 26.9% of cell lines).

Located in mitochondrion.

Source: NCBI Gene 125228 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 43 total
• Cancer dependency (DepMap): dependent in 26.9% of screened cell lines
• MANE Select transcript: NM_152352

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28346
Approved symbol	MIMS1
Name	mitochondrial inner membrane scaffold 1
Location	18p11.21
Locus type	gene with protein product
Status	Approved
Aliases	MGC24180, HsT2329
Ensembl gene	ENSG00000177150
Ensembl biotype	protein_coding
OMIM	617975
Entrez	125228

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000322247, ENST00000402563, ENST00000585785, ENST00000588475, ENST00000589346, ENST00000591269, ENST00000592976, ENST00000651643, ENST00000910032, ENST00000963450, ENST00000963451, ENST00000963452

RefSeq mRNA: 2 — MANE Select: NM_152352 NM_001098801, NM_152352

CCDS: CCDS11866

Canonical transcript exons

ENST00000651643 — 4 exons

Exon	Start	End
ENSE00003646262	13681605	13682105
ENSE00003843239	13726329	13726558
ENSE00003893689	13663347	13666713
ENSE00003895827	13671862	13671973

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 95.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.4179 / max 163.5721, expressed in 1816 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
171290	18.4531	1815
171287	0.4839	240
171288	0.2134	92
171286	0.1898	72
171289	0.0777	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	95.97	gold quality
amniotic fluid	UBERON:0000173	95.47	gold quality
heart right ventricle	UBERON:0002080	92.28	gold quality
vastus lateralis	UBERON:0001379	92.23	gold quality
endothelial cell	CL:0000115	92.11	gold quality
quadriceps femoris	UBERON:0001377	91.77	gold quality
myocardium	UBERON:0002349	91.76	gold quality
cardiac muscle of right atrium	UBERON:0003379	90.32	gold quality
body of tongue	UBERON:0011876	90.19	gold quality
biceps brachii	UBERON:0001507	89.47	gold quality
skeletal muscle tissue	UBERON:0001134	89.18	gold quality
deltoid	UBERON:0001476	88.94	gold quality
muscle tissue	UBERON:0002385	88.32	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	88.11	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.99	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	87.64	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.49	gold quality
tibialis anterior	UBERON:0001385	87.43	gold quality
cartilage tissue	UBERON:0002418	87.39	gold quality
cardiac ventricle	UBERON:0002082	87.18	gold quality
heart left ventricle	UBERON:0002084	87.02	gold quality
epithelial cell of pancreas	CL:0000083	86.43	silver quality
muscle of leg	UBERON:0001383	86.39	gold quality
gastrocnemius	UBERON:0001388	86.11	gold quality
oviduct epithelium	UBERON:0004804	85.99	gold quality
heart	UBERON:0000948	85.80	gold quality
cardiac atrium	UBERON:0002081	85.58	gold quality
tongue	UBERON:0001723	85.44	gold quality
right atrium auricular region	UBERON:0006631	85.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.93	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.94
E-GEOD-81383	no	1003.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

175 targeting MIMS1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4803	99.98	71.99	3117
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-607	99.97	73.62	5593
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-651-3P	99.94	73.48	5177
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

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 26.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

• Genetic variation near FAM210A, a gene of previously unknown function, was strongly associated with both appendicular and whole body lean mass, as well as bone mineral density. (PMID:29618611)
• Circular RNA cFAM210A, degradable by HBx, inhibits HCC tumorigenesis by suppressing YBX1 transactivation. (PMID:37907737)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam210aa	ENSDARG00000035985
danio_rerio	fam210ab	ENSDARG00000040186
mus_musculus	Fam210a	ENSMUSG00000038121
rattus_norvegicus	Fam210a	ENSRNOG00000080800
drosophila_melanogaster	CG14613	FBGN0031188
caenorhabditis_elegans		WBGENE00013239

Paralogs (1): FAM210B (ENSG00000124098)

Protein

Protein identifiers

Protein FAM210A — Q96ND0 (reviewed: Q96ND0)

All UniProt accessions (4): Q96ND0, K7EK00, K7EPG9, K7ERQ2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the structure and strength of both muscle and bone.

Subunit / interactions. Interacts with ATAD3A.

Subcellular location. Membrane. Mitochondrion. Cytoplasm.

Similarity. Belongs to the FAM210 family.

RefSeq proteins (2): NP_001092271, NP_689565* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009688	FAM210A/B-like_dom	Domain
IPR045866	FAM210A/B-like	Family

Pfam: PF06916

UniProt features (10 total): sequence variant 4, chain 1, transmembrane region 1, domain 1, region of interest 1, coiled-coil region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96ND0-F1	64.73	0.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 89 (showing top): GTTAAAG_MIR302B, GTGCCTT_MIR506, WEI_MYCN_TARGETS_WITH_E_BOX, TGCCTTA_MIR124A, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B, ER_Q6_01, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP, KRIEG_HYPOXIA_NOT_VIA_KDM3A, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, CREB3L4_TARGET_GENES, DIDO1_TARGET_GENES, ID2_TARGET_GENES, KAT5_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): cytoplasm (GO:0005737), mitochondrion (GO:0005739), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
intracellular anatomical structure	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

708 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MIMS1	ZBTB40	Q9NUA8	592
MIMS1	DCDC1	P59894	527
MIMS1	CPED1	A4D0V7	507
MIMS1	SLC25A13	Q9UJS0	505
MIMS1	STARD3NL	O95772	479
MIMS1	SPTBN1	Q01082	478
MIMS1	HIBADH	P31937	454
MIMS1	MEPE	Q9NQ76	446
MIMS1	HROB	Q8N3J3	445
MIMS1	ATAD3A	Q9NVI7	429
MIMS1	WNT16	Q9UBV4	400
MIMS1	AKAP11	Q9UKA4	380
MIMS1	OR8H3	Q8N146	377
MIMS1	FTCDNL1	E5RQL4	373
MIMS1	DNAAF8	Q8IYS4	366
MIMS1	ARMCX2	Q7L311	366

IntAct

31 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CD63	LGALS8	psi-mi:“MI:0914”(association)	0.530
NPTN	TNPO2	psi-mi:“MI:0914”(association)	0.530
IFT52	IFT56	psi-mi:“MI:0914”(association)	0.510
CD300C	ATP12A	psi-mi:“MI:0914”(association)	0.350
ATAD3A	TMEM223	psi-mi:“MI:0914”(association)	0.350
BABAM1	PYCR3	psi-mi:“MI:0914”(association)	0.350
STK32C	ILVBL	psi-mi:“MI:0914”(association)	0.350
MGARP	BTAF1	psi-mi:“MI:0914”(association)	0.350
HCST	TMEM120B	psi-mi:“MI:0914”(association)	0.350
EIF2B5	GOLIM4	psi-mi:“MI:0914”(association)	0.350
GPR182	SLC12A8	psi-mi:“MI:0914”(association)	0.350
BRICD5	TMEM131L	psi-mi:“MI:0914”(association)	0.350
ASIC4	TMEM131L	psi-mi:“MI:0914”(association)	0.350
LCN6	POTEF	psi-mi:“MI:0914”(association)	0.350
SLC1A1	UBXN8	psi-mi:“MI:0914”(association)	0.350
NAAA	HAX1	psi-mi:“MI:0914”(association)	0.350
RAMP3	MGST3	psi-mi:“MI:0914”(association)	0.350
EIF2B5	KCNN4	psi-mi:“MI:0914”(association)	0.350
HLA-DRA	MGRN1	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350
SLC1A1	SCD	psi-mi:“MI:0914”(association)	0.350
SLC1A2	UBXN8	psi-mi:“MI:0914”(association)	0.350
SLC39A2	AGPAT2	psi-mi:“MI:0914”(association)	0.350
FAM210A	IFT52	psi-mi:“MI:0915”(physical association)	0.000
FAM210A	menB	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (38): FAM210A (Affinity Capture-RNA), FAM210A (Affinity Capture-RNA), FAM210A (Affinity Capture-MS), FAM210A (Affinity Capture-MS), FAM210A (Affinity Capture-MS), FAM210A (Affinity Capture-MS), COPA (Affinity Capture-MS), COPB2 (Affinity Capture-MS), RCN2 (Affinity Capture-MS), COPE (Affinity Capture-MS), MYL6 (Affinity Capture-MS), DNAJA2 (Affinity Capture-MS), LDHB (Affinity Capture-MS), FAM210A (Affinity Capture-MS), IFT52 (Affinity Capture-MS)

ESM2 similar proteins: A2R3F3, A4IJ20, A6ZYZ4, A7THM1, D6WIX5, O95202, P37293, P53220, Q03079, Q04172, Q05B67, Q0V9J0, Q0VA06, Q1LY46, Q1MTD4, Q2KI30, Q4ICM9, Q4QQV3, Q4WKN3, Q59VW7, Q5CZQ0, Q5M7E0, Q5RE99, Q5U2X7, Q5XIJ4, Q5XIN6, Q5XKA2, Q5XTS1, Q5ZK33, Q5ZML6, Q63ZZ0, Q6BJ94, Q6BVK1, Q6CLZ3, Q6CUA2, Q6DC58, Q6FK33, Q753C3, Q8BGY7, Q8CCM6

Diamond homologs: A4IJ20, Q05B67, Q1MTD4, Q5CZQ0, Q5M7E0, Q5RE99, Q5XIJ4, Q5ZML6, Q8BGY7, Q96ND0, Q9D8B6, Q96KR6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1394 predictions. Top by Δscore:

Variant	Effect	Δscore
18:13666709:GCAAT:G	acceptor_gain	1.0000
18:13666710:CAAT:C	acceptor_gain	1.0000
18:13666710:CAATC:C	acceptor_gain	1.0000
18:13666711:AAT:A	acceptor_gain	1.0000
18:13666711:AATCT:A	acceptor_loss	1.0000
18:13666712:AT:A	acceptor_gain	1.0000
18:13666713:TCTTA:T	acceptor_loss	1.0000
18:13666714:C:CC	acceptor_gain	1.0000
18:13666715:T:A	acceptor_loss	1.0000
18:13666715:T:C	acceptor_gain	1.0000
18:13666715:T:TC	acceptor_gain	1.0000
18:13666720:C:CT	acceptor_gain	1.0000
18:13666721:A:T	acceptor_gain	1.0000
18:13666727:C:CT	acceptor_gain	1.0000
18:13666731:C:CT	acceptor_gain	0.9900
18:13667915:AGC:A	donor_gain	0.9900
18:13670914:TGA:T	donor_gain	0.9900
18:13671969:CTCCT:C	acceptor_gain	0.9900
18:13671974:C:CC	acceptor_gain	0.9900
18:13681603:A:AC	donor_gain	0.9900
18:13681604:C:CC	donor_gain	0.9900
18:13681604:CTT:C	donor_gain	0.9900
18:13682103:CTT:C	acceptor_gain	0.9900
18:13682106:C:CC	acceptor_gain	0.9900
18:13726323:TGCTA:T	donor_loss	0.9900
18:13726324:GCTAC:G	donor_loss	0.9900
18:13726325:CTA:C	donor_loss	0.9900
18:13726326:TACC:T	donor_loss	0.9900
18:13726328:CCT:C	donor_gain	0.9900
18:13726328:CCTCT:C	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000015528 (18:13666012 C>T), RS1000073485 (18:13686266 G>A), RS1000136170 (18:13714328 C>G,T), RS1000196376 (18:13714070 G>A), RS1000214937 (18:13681166 T>G), RS1000215425 (18:13668166 C>T), RS1000274305 (18:13720598 A>G), RS1000280335 (18:13726478 C>G,T), RS1000312172 (18:13707744 T>C), RS1000395901 (18:13726222 G>C), RS1000415726 (18:13726258 A>G), RS1000440877 (18:13686943 T>G), RS1000450917 (18:13683447 T>C), RS1000512414 (18:13689148 G>A,T), RS1000530746 (18:13712594 CAA>C)

Disease associations

OMIM: gene MIM:617975 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST006288_300	Heel bone mineral density	4.000000e-43
GCST006288_366	Heel bone mineral density	6.000000e-18
GCST006288_67	Heel bone mineral density	2.000000e-24
GCST006423_14	Fracture	1.000000e-18
GCST006979_264	Heel bone mineral density	3.000000e-123
GCST006979_265	Heel bone mineral density	5.000000e-12
GCST006980_13	Fracture	2.000000e-27
GCST007691_14	Femoral neck bone mineral density	5.000000e-08
GCST009870_24	Calcific aortic valve stenosis	6.000000e-06
GCST90011900_154	Serum alkaline phosphatase levels	1.000000e-08
GCST90013406_203	Liver enzyme levels (alkaline phosphatase)	2.000000e-13

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density
EFO:0007785	femoral neck bone mineral density
EFO:0000266	aortic stenosis
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases methylation	4
Cadmium Chloride	increases abundance, increases expression	4
Aflatoxin B1	decreases methylation, increases methylation, decreases expression	3
Arsenic	increases abundance, increases expression, affects cotreatment	2
Formaldehyde	decreases expression	2
Cyclosporine	increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
chloroacetaldehyde	increases expression	1
triphenyl phosphate	affects expression	1
glycidyl methacrylate	increases expression	1
sodium arsenate	increases abundance, increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
beta-lapachone	decreases expression	1
arsenite	increases reaction, affects binding	1
1,6-hexamethylene diisocyanate	increases methylation	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	increases expression, affects cotreatment	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
Rosiglitazone	affects cotreatment, increases expression, decreases reaction	1
Resveratrol	affects cotreatment, increases expression	1
Pioglitazone	increases expression, affects cotreatment	1
Sunitinib	increases expression	1
Troglitazone	affects cotreatment, increases expression, decreases reaction	1
Cidofovir	increases expression	1

Clinical trials (associated diseases)

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