MTFR1

Summary

MTFR1 (mitochondrial fission regulator 1, HGNC:29510) is a protein-coding gene on chromosome 8q13.1, encoding Mitochondrial fission regulator 1 (Q15390). May play a role in mitochondrial aerobic respiration.

This gene encodes a mitochondrial protein that is characterized by a poly-proline rich region. A chicken homolog of this protein promotes mitochondrial fission and the mouse homolog protects cells from oxidative stress. A related pseudogene of this gene is found on chromosome X.

Source: NCBI Gene 9650 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 111 total
• MANE Select transcript: NM_014637

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29510
Approved symbol	MTFR1
Name	mitochondrial fission regulator 1
Location	8q13.1
Locus type	gene with protein product
Status	Approved
Aliases	CHPPR, KIAA0009, FAM54A2
Ensembl gene	ENSG00000066855
Ensembl biotype	protein_coding
OMIM	619414
Entrez	9650

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 20 protein_coding, 7 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000262146, ENST00000424808, ENST00000458689, ENST00000517944, ENST00000518352, ENST00000518636, ENST00000518800, ENST00000520398, ENST00000521247, ENST00000522239, ENST00000523158, ENST00000523170, ENST00000523222, ENST00000527155, ENST00000527553, ENST00000867674, ENST00000867675, ENST00000867676, ENST00000867677, ENST00000867678, ENST00000867679, ENST00000867680, ENST00000867681, ENST00000867682, ENST00000867683, ENST00000935996, ENST00000935997, ENST00000935998, ENST00000971080, ENST00000971081

RefSeq mRNA: 19 — MANE Select: NM_014637 NM_001145838, NM_001145839, NM_001413068, NM_001413069, NM_001413070, NM_001413071, NM_001413073, NM_001413074, NM_001413075, NM_001413076, NM_001413077, NM_001413078, NM_001413079, NM_001413080, NM_001413081, NM_001413082, NM_001413083, NM_001413084, NM_014637

CCDS: CCDS55240, CCDS6182

Canonical transcript exons

ENST00000262146 — 8 exons

Exon	Start	End
ENSE00002118474	65708976	65710562
ENSE00002130480	65644734	65644784
ENSE00003464178	65707843	65708011
ENSE00003505497	65693644	65693759
ENSE00003520163	65707010	65707256
ENSE00003600708	65682353	65682451
ENSE00003651941	65669873	65670018
ENSE00003663613	65704694	65704929

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 97.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.5008 / max 487.5155, expressed in 1795 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
89146	18.2300	1792
89147	2.0238	1123
89149	0.1317	39
89145	0.1037	23
89148	0.0115	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	97.62	gold quality
nephron tubule	UBERON:0001231	95.90	gold quality
left testis	UBERON:0004533	94.25	gold quality
right testis	UBERON:0004534	93.76	gold quality
jejunal mucosa	UBERON:0000399	93.66	gold quality
kidney epithelium	UBERON:0004819	93.57	gold quality
oocyte	CL:0000023	93.38	gold quality
renal glomerulus	UBERON:0000074	92.93	gold quality
testis	UBERON:0000473	92.87	gold quality
metanephric glomerulus	UBERON:0004736	92.81	gold quality
right atrium auricular region	UBERON:0006631	92.81	gold quality
liver	UBERON:0002107	92.65	gold quality
adult organism	UBERON:0007023	92.64	gold quality
right lobe of thyroid gland	UBERON:0001119	92.61	gold quality
right lobe of liver	UBERON:0001114	92.52	gold quality
left lobe of thyroid gland	UBERON:0001120	92.46	gold quality
body of pancreas	UBERON:0001150	92.18	gold quality
heart left ventricle	UBERON:0002084	92.15	gold quality
oral cavity	UBERON:0000167	92.14	gold quality
hindlimb stylopod muscle	UBERON:0004252	92.08	gold quality
cardiac ventricle	UBERON:0002082	91.96	gold quality
islet of Langerhans	UBERON:0000006	91.85	gold quality
kidney	UBERON:0002113	91.81	gold quality
cortex of kidney	UBERON:0001225	91.77	gold quality
thyroid gland	UBERON:0002046	91.75	gold quality
minor salivary gland	UBERON:0001830	91.68	gold quality
rectum	UBERON:0001052	91.63	gold quality
pancreas	UBERON:0001264	91.61	gold quality
amniotic fluid	UBERON:0000173	91.60	gold quality
esophagus squamous epithelium	UBERON:0006920	91.57	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting MTFR1, 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-340-5P	100.00	72.50	4437
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-4682	100.00	68.89	1258
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-126-5P	100.00	72.71	3180
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4422	99.72	72.07	2908

Literature-anchored findings (GeneRIF, showing 5)

• presents partial sequence of a human homolog of chicken MTFR1 (PMID:12359332)
• reports full-length mRNA sequence of human MTFR1. (PMID:15389597)
• reports the role of mouse Mtfr1 in protecting cells from reactive oxygen species using Mtfr1-deficient mice. (PMID:17709566)
• Our results suggested that miR-324-5p protects against oxidative stress-induced endothelial progenitor cells injury by regulating Mtfr1. (PMID:31066044)
• Overexpression of MTFR1 promotes cancer progression and drug-resistance on cisplatin and is related to the immune microenvironment in lung adenocarcinoma. (PMID:38170222)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mtfr1	ENSDARG00000045304
mus_musculus	Mtfr1	ENSMUSG00000027601
rattus_norvegicus	LOC120101654	ENSRNOG00000021359

Paralogs (2): MTFR1L (ENSG00000117640), MTFR2 (ENSG00000146410)

Protein

Protein identifiers

Mitochondrial fission regulator 1 — Q15390 (reviewed: Q15390)

Alternative names: Chondrocyte protein with a poly-proline region

All UniProt accessions (5): Q15390, E5RIB6, H0YBZ4, H0YF01, H7C5V5

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in mitochondrial aerobic respiration. May also regulate mitochondrial organization and fission.

Subcellular location. Mitochondrion.

Similarity. Belongs to the MTFR1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q15390-1	1	yes
Q15390-2	2

RefSeq proteins (19): NP_001139310, NP_001139311, NP_001399997, NP_001399998, NP_001399999, NP_001400000, NP_001400002, NP_001400003, NP_001400004, NP_001400005, NP_001400006, NP_001400007, NP_001400008, NP_001400009, NP_001400010, NP_001400011, NP_001400012, NP_001400013, NP_055452* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007972	Mtfr1	Family

Pfam: PF05308

UniProt features (11 total): region of interest 3, compositionally biased region 2, transit peptide 1, chain 1, sequence conflict 1, coiled-coil region 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15390-F1	65.95	0.12

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 119

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 164 (showing top): TGCGCANK_UNKNOWN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, CMYB_01, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, WEI_MYCN_TARGETS_WITH_E_BOX, ONKEN_UVEAL_MELANOMA_UP, GOBP_ORGANELLE_FISSION, GOBP_MITOCHONDRIAL_FISSION, MODULE_206, GOBP_CELLULAR_RESPIRATION, ACEVEDO_LIVER_CANCER_UP, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP, chr8q13, FARMER_BREAST_CANCER_CLUSTER_2

GO Biological Process (3): mitochondrial fission (GO:0000266), mitochondrion organization (GO:0007005), aerobic respiration (GO:0009060)

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

GO Cellular Component (3): mitochondrion (GO:0005739), cytosol (GO:0005829), plasma membrane (GO:0005886)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
mitochondrion organization	1
organelle fission	1
organelle organization	1
cellular respiration	1
binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1209 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MTFR1	GPR19	Q15760	520
MTFR1	TEC	P42680	460
MTFR1	CPQ	Q9Y646	448
MTFR1	EPHA8	P29322	406
MTFR1	SFXN4	Q6P4A7	395
MTFR1	PDE7A	Q13946	388
MTFR1	CAPN12	Q6ZSI9	371
MTFR1	GARIN5A	Q6IPT2	356
MTFR1	ERICH6B	Q5W0A0	355
MTFR1	ALDH18A1	P54886	351
MTFR1	NOSIP	Q9Y314	336
MTFR1	XPNPEP2	O43895	333
MTFR1	C20orf96	Q9NUD7	332
MTFR1	ARID4A	P29374	331
MTFR1	ARID4B	Q4LE39	331

IntAct

59 interactions, top by confidence:

A	B	Type	Score
MTFR1	DIABLO	psi-mi:“MI:0915”(physical association)	0.740
CCDC120	AIP	psi-mi:“MI:0914”(association)	0.640
MTFR1	SYT16	psi-mi:“MI:0915”(physical association)	0.560
IL13RA2	METTL15	psi-mi:“MI:0914”(association)	0.530
MIA2	RGPD3	psi-mi:“MI:0914”(association)	0.530
ODAD3	CCDC22	psi-mi:“MI:0914”(association)	0.530
FGL2	PCNT	psi-mi:“MI:0914”(association)	0.530
HTRA2	HAX1	psi-mi:“MI:2364”(proximity)	0.420
MTFR1	CTSO	psi-mi:“MI:0915”(physical association)	0.400
DUSP23	MTFR1	psi-mi:“MI:0915”(physical association)	0.370
Myh9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
CAPZA2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
ZNG1A	AGAP1	psi-mi:“MI:0914”(association)	0.350
P2RX5	NOP56	psi-mi:“MI:0914”(association)	0.350
ATG14	MAP4K4	psi-mi:“MI:0914”(association)	0.350
COLEC11	COL6A1	psi-mi:“MI:0914”(association)	0.350
DIABLO	GFER	psi-mi:“MI:0914”(association)	0.350
CENPO	ITGB3BP	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
JAK3	PIK3R2	psi-mi:“MI:0914”(association)	0.350
ACTB	ENAH	psi-mi:“MI:0914”(association)	0.350
ACTG1	ENAH	psi-mi:“MI:0914”(association)	0.350
CALD1		psi-mi:“MI:0914”(association)	0.350
PFN1	WASL	psi-mi:“MI:0914”(association)	0.350

BioGRID (96): MTFR1 (Affinity Capture-RNA), MTFR1 (Affinity Capture-RNA), MTFR1 (Affinity Capture-RNA), MTFR1 (Affinity Capture-RNA), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS)

ESM2 similar proteins: A0JP43, A1YEW9, A2D4U8, A2D5N1, A2D671, A2T6K9, A8T6P4, B8AE37, F6QRE9, G3V9A7, O60238, P48785, P79149, Q0IIJ3, Q0P6D6, Q15170, Q15361, Q15390, Q2KIJ9, Q3T013, Q3ULM0, Q3ZBJ9, Q4V7L5, Q5H9J7, Q5NVG8, Q5PPP3, Q5PR69, Q5RFN3, Q5W0A0, Q66HD8, Q67XL4, Q6K678, Q86X53, Q8BP27, Q8BPM6, Q8C627, Q8N4S0, Q8R5H6, Q91W45, Q921P9

Diamond homologs: F1RCE7, G3V9A7, Q08BD8, Q0VFP3, Q15390, Q3ZBW7, Q4V7T5, Q5R3Z9, Q5RFN3, Q5XII9, Q6GP48, Q7T3E8, Q8VED8, Q99MB2, Q9CWE0, Q9H019, Q9PTD5, B0K035, Q58CR1, Q6P444

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	80
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3591 predictions. Top by Δscore:

Variant	Effect	Δscore
8:65669871:A:AG	acceptor_gain	1.0000
8:65669872:G:GA	acceptor_gain	1.0000
8:65669872:GTGT:G	acceptor_gain	1.0000
8:65693755:CTAAG:C	donor_loss	1.0000
8:65693756:TAAG:T	donor_loss	1.0000
8:65693757:AAG:A	donor_loss	1.0000
8:65693758:AGGTT:A	donor_loss	1.0000
8:65693760:G:T	donor_loss	1.0000
8:65693761:T:A	donor_loss	1.0000
8:65704691:CAG:C	acceptor_loss	1.0000
8:65704692:AGGAC:A	acceptor_loss	1.0000
8:65704693:GGACA:G	acceptor_gain	1.0000
8:65704827:G:GT	donor_gain	1.0000
8:65704930:G:GC	donor_loss	1.0000
8:65704930:GTCT:G	donor_gain	1.0000
8:65704931:TCT:T	donor_gain	1.0000
8:65704934:G:GG	donor_gain	1.0000
8:65707007:TA:T	acceptor_loss	1.0000
8:65707008:A:AG	acceptor_gain	1.0000
8:65707008:AGGT:A	acceptor_gain	1.0000
8:65707009:G:GG	acceptor_gain	1.0000
8:65707009:GGT:G	acceptor_gain	1.0000
8:65707009:GGTG:G	acceptor_gain	1.0000
8:65707254:GAG:G	donor_gain	1.0000
8:65707255:AGG:A	donor_loss	1.0000
8:65707256:GGTG:G	donor_loss	1.0000
8:65707257:G:GG	donor_gain	1.0000
8:65707257:GT:G	donor_loss	1.0000
8:65707258:T:A	donor_loss	1.0000
8:65707832:A:AG	acceptor_gain	1.0000

AlphaMissense

2166 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:65707922:T:C	F282L	0.998
8:65707924:T:A	F282L	0.998
8:65707924:T:G	F282L	0.998
8:65704864:T:C	L151P	0.997
8:65682389:A:C	S35R	0.996
8:65682391:T:A	S35R	0.996
8:65682391:T:G	S35R	0.996
8:65682399:G:C	R38T	0.996
8:65682399:G:T	R38M	0.996
8:65682400:G:C	R38S	0.996
8:65682400:G:T	R38S	0.996
8:65704873:T:C	L154P	0.996
8:65704887:G:C	A159P	0.996
8:65682408:G:A	G41D	0.994
8:65707901:G:C	A275P	0.994
8:65704873:T:A	L154H	0.993
8:65707911:T:C	L278P	0.993
8:65682447:T:C	F54S	0.992
8:65704852:T:A	L147H	0.992
8:65704852:T:C	L147P	0.991
8:65707907:G:C	A277P	0.991
8:65704864:T:A	L151H	0.990
8:65707899:T:A	I274K	0.989
8:65707911:T:A	L278Q	0.989
8:65682439:A:C	R51S	0.988
8:65682439:A:T	R51S	0.988
8:65682396:T:A	V37E	0.987
8:65682407:G:C	G41R	0.986
8:65682417:T:C	L44S	0.986
8:65707923:T:C	F282S	0.986

dbSNP variants (sampled 300 via entrez): RS1000032536 (8:65713314 A>T), RS1000033505 (8:65699211 A>G), RS1000038298 (8:65659511 T>C), RS1000043727 (8:65663926 C>T), RS1000059991 (8:65684642 C>T), RS1000061339 (8:65652319 G>A), RS1000070490 (8:65747028 A>C,G,T), RS1000131448 (8:65754997 A>G), RS1000208572 (8:65729225 G>C), RS1000211140 (8:65706154 A>T), RS1000225923 (8:65754615 C>T), RS1000242289 (8:65711065 C>G,T), RS1000260631 (8:65666778 G>A), RS1000262914 (8:65756240 G>A), RS1000272324 (8:65713759 T>C)

Disease associations

OMIM: gene MIM:619414 | 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
GCST009391_428	Metabolite levels	7.000000e-06
GCST009391_778	Metabolite levels	8.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010384	phosphatidylcholine 38:2 measurement
EFO:0010393	sphingomyelin 18:0 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
Cyclosporine	increases expression	3
Air Pollutants	decreases expression, affects cotreatment, increases abundance, increases oxidation	2
Quercetin	decreases phosphorylation, decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Tretinoin	decreases expression	2
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	decreases expression	1
beta-lapachone	decreases expression, increases expression	1
arsenite	increases reaction, affects binding	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
sulindac sulfide	increases expression	1
benzo(e)pyrene	increases methylation	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
corosolic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
picoxystrobin	increases expression	1
Decitabine	affects expression	1
Sunitinib	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects expression	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1

Clinical trials (associated diseases)

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