MCCD1

Summary

MCCD1 (mitochondrial coiled-coil domain 1, HGNC:20668) is a protein-coding gene on chromosome 6p21.33, encoding Mitochondrial coiled-coil domain protein 1 (P59942).

Located in mitochondrion.

Source: NCBI Gene 401250 — RefSeq curated summary.

At a glance

• GWAS associations: 25
• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_001011700

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20668
Approved symbol	MCCD1
Name	mitochondrial coiled-coil domain 1
Location	6p21.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204511
Ensembl biotype	protein_coding
OMIM	609624
Entrez	401250

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000376191

RefSeq mRNA: 1 — MANE Select: NM_001011700 NM_001011700

CCDS: CCDS34396

Canonical transcript exons

ENST00000376191 — 2 exons

Exon	Start	End
ENSE00001791348	31528962	31529185
ENSE00001832583	31529747	31530232

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 94.50.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1472 / max 105.7345, expressed in 8 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66888	0.1013	8
66889	0.0263	3
66890	0.0195	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adult mammalian kidney	UBERON:0000082	94.50	gold quality
kidney	UBERON:0002113	87.77	gold quality
metanephros cortex	UBERON:0010533	84.18	gold quality
cortex of kidney	UBERON:0001225	77.48	gold quality
stromal cell of endometrium	CL:0002255	52.06	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	51.75	silver quality
sural nerve	UBERON:0015488	49.50	silver quality
calcaneal tendon	UBERON:0003701	48.13	silver quality
leukocyte	CL:0000738	47.24	gold quality
monocyte	CL:0000576	46.70	gold quality
adrenal tissue	UBERON:0018303	44.20	silver quality
muscle of leg	UBERON:0001383	42.91	gold quality
granulocyte	CL:0000094	42.76	silver quality
hindlimb stylopod muscle	UBERON:0004252	42.32	gold quality
gastrocnemius	UBERON:0001388	42.28	gold quality
skeletal muscle tissue	UBERON:0001134	41.89	gold quality
blood	UBERON:0000178	40.80	silver quality
bone marrow cell	CL:0002092	39.69	gold quality
rectum	UBERON:0001052	39.08	silver quality
muscle tissue	UBERON:0002385	38.76	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
bone marrow	UBERON:0002371	37.03	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	36.99	silver quality
Brodmann (1909) area 9	UBERON:0013540	36.98	silver quality
thoracic mammary gland	UBERON:0005200	36.76	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
endometrium	UBERON:0001295	35.25	gold quality
liver	UBERON:0002107	34.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting MCCD1, 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-302E	99.96	70.74	2669
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-154-5P	98.92	66.65	733
HSA-MIR-4260	98.78	65.37	848
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-655-5P	98.74	65.93	888
HSA-MIR-6769B-5P	98.73	64.91	1092
HSA-MIR-5572	98.55	65.84	970
HSA-MIR-6819-5P	97.96	66.59	1071
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-6737-5P	97.75	66.54	1044
HSA-MIR-6812-5P	97.56	65.39	1059
HSA-MIR-4253	97.48	65.11	692
HSA-MIR-3173-5P	97.35	65.82	1282
HSA-MIR-6799-3P	97.35	65.60	1302
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-2909	96.36	67.30	562
HSA-MIR-4296	96.35	63.55	1233
HSA-MIR-6747-5P	96.17	64.99	743

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Mitochondrial coiled-coil domain protein 1 — P59942 (reviewed: P59942)

All UniProt accessions (2): P59942, A0A1U9X802

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Mitochondrion.

Tissue specificity. Widely expressed. Expressed in adult and fetal liver, kidney and lung. Expressed in fetal brain. Weakly expressed in fetal spleen.

RefSeq proteins (1): NP_001011700* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031438	MCCD1	Family

Pfam: PF15707

UniProt features (8 total): sequence variant 3, transit peptide 1, chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P59942-F1	66.57	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 11 (showing top): MIR204_5P, MIR211_5P, MIR5572, MIR6819_5P, MIR6737_5P, MIR655_5P, MIR2909, MIR6747_5P, chr6p21, AGCACTT_MIR93_MIR302A_MIR302B_MIR302C_MIR302D_MIR372_MIR373_MIR520E_MIR520A_MIR526B_MIR520B_MIR520C_MIR520D, GOCC_MITOCHONDRION

GO Biological Process (0):

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

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

228 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MCCD1	MICB	P79525	568
MCCD1	NFKBIL1	Q9UBC1	544
MCCD1	PSORS1C1	Q9UIG5	495
MCCD1	OR10C1	Q96KK4	488
MCCD1	ATP6V1G2	O95670	473
MCCD1	FBLL1	A6NHQ2	465
MCCD1	HLA-DQB2	P05538	461
MCCD1	DDX39B	Q13838	411
MCCD1	KIFC1	Q9BW19	410
MCCD1	ZBTB9	Q96C00	400
MCCD1	RPP21	Q9H633	400
MCCD1	LRRC46	Q96FV0	399
MCCD1	ADGRF2P	Q8IZF7	399
MCCD1	GTF3C6	Q969F1	373
MCCD1	RIMKLA	Q8IXN7	372

IntAct

86 interactions, top by confidence:

A	B	Type	Score
CTNNA3	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
RIPPLY1	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
FNDC3B	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	USP20	psi-mi:“MI:0915”(physical association)	0.560
USHBP1	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
PPP1R16A	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
QARS1	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
ZNF765	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
USP20	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
KRT26	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	CTNNA3	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	ZNF417	psi-mi:“MI:0915”(physical association)	0.560
MX1	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	KANK2	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	ZNF765	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	P4HA3	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	RIPPLY1	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	ZNF587	psi-mi:“MI:0915”(physical association)	0.560
	MCCD1	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	MKRN3	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	BFSP2	psi-mi:“MI:0915”(physical association)	0.560
MCCD1	FNDC3B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (30): MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid), MCCD1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVZ6, A0A1W2PR82, A0A286YDK6, A2A9F4, A6H7B4, A6NDZ8, A6NE82, A6NJ08, A6NJJ6, A6QP24, D2H5P6, D4A8G9, E1BLZ4, E1C7U0, P59942, Q0P5M0, Q2KIL8, Q32KP7, Q3B8N5, Q3T0X9, Q5DU37, Q5EAA5, Q5JYT7, Q5M844, Q68DK2, Q68FX5, Q6AY88, Q6GQV0, Q6P0A1, Q7TSF4, Q86WR6, Q8BII1, Q8BWG4, Q8CF25, Q8N4L8, Q8NAA5, Q8NAX2, Q8NHZ7, Q8TAP8, Q8VEA7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

110 predictions. Top by Δscore:

Variant	Effect	Δscore
6:31529740:T:A	acceptor_gain	0.9800
6:31529743:CCA:C	acceptor_loss	0.9800
6:31529744:CA:C	acceptor_loss	0.9800
6:31529745:AG:A	acceptor_gain	0.9800
6:31529746:G:GT	acceptor_loss	0.9800
6:31529746:GG:G	acceptor_gain	0.9800
6:31529184:GG:G	donor_gain	0.9700
6:31529185:GG:G	donor_gain	0.9700
6:31529745:A:AG	acceptor_gain	0.9700
6:31529746:G:GG	acceptor_gain	0.9700
6:31529185:GGTAA:G	donor_loss	0.9600
6:31529186:G:GG	donor_gain	0.9600
6:31529745:AGG:A	acceptor_gain	0.9600
6:31529746:GGG:G	acceptor_gain	0.9600
6:31529746:GGGC:G	acceptor_gain	0.9600
6:31529746:GGGCC:G	acceptor_gain	0.9600
6:31529188:AAGTG:A	donor_loss	0.9400
6:31529645:G:T	donor_gain	0.9400
6:31529183:AGG:A	donor_gain	0.9300
6:31529184:GGG:G	donor_gain	0.9300
6:31529182:CAGG:C	donor_gain	0.9100
6:31529164:G:T	donor_gain	0.8700
6:31529181:CCAGG:C	donor_gain	0.8700
6:31529164:G:GT	donor_gain	0.8600
6:31529651:G:GA	donor_gain	0.8500
6:31529189:AGTGG:A	donor_loss	0.8400
6:31529740:T:TA	acceptor_loss	0.8100
6:31529645:G:GT	donor_gain	0.8000
6:31529650:T:TA	donor_gain	0.7900
6:31529646:A:T	donor_gain	0.7800

AlphaMissense

760 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:31529890:G:C	K105N	0.978
6:31529890:G:T	K105N	0.978
6:31529875:G:C	K100N	0.954
6:31529875:G:T	K100N	0.954
6:31529889:A:T	K105M	0.935
6:31529886:T:C	L104P	0.927
6:31529889:A:C	K105T	0.912
6:31529822:G:C	A83P	0.893
6:31529871:T:C	L99P	0.891
6:31529796:T:C	L74S	0.889
6:31529884:G:C	K103N	0.887
6:31529884:G:T	K103N	0.887
6:31529851:G:C	W92C	0.878
6:31529851:G:T	W92C	0.878
6:31529874:A:T	K100M	0.876
6:31529898:T:C	M108T	0.873
6:31529834:G:A	G87R	0.870
6:31529834:G:C	G87R	0.870
6:31529881:G:C	Q102H	0.867
6:31529881:G:T	Q102H	0.867
6:31529793:T:C	L73S	0.863
6:31529874:A:C	K100T	0.858
6:31529826:T:C	L84P	0.854
6:31529865:T:C	L97P	0.854
6:31529834:G:T	G87W	0.850
6:31529873:A:G	K100E	0.843
6:31529806:G:C	Q77H	0.836
6:31529806:G:T	Q77H	0.836
6:31529871:T:A	L99H	0.834
6:31529899:G:A	M108I	0.834

dbSNP variants (sampled 300 via entrez): RS1000639768 (6:31530616 T>A), RS1000684336 (6:31530463 C>T), RS1002923958 (6:31528281 T>C), RS1003095539 (6:31530211 C>G,T), RS1003403370 (6:31529226 T>C), RS1004137882 (6:31528627 T>C), RS1005088450 (6:31527027 G>A,C), RS1005249340 (6:31529627 G>A,C), RS1006669311 (6:31528256 A>G), RS1007969882 (6:31528122 C>G,T), RS1008038587 (6:31527573 G>T), RS1008072632 (6:31529340 C>T), RS1008091082 (6:31527914 A>T), RS1009112099 (6:31528480 T>C), RS1010776298 (6:31529281 C>A,T)

Disease associations

OMIM: gene MIM:609624 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

25 associations (top):

Study	Trait	p-value
GCST000308_1	AIDS progression	3.000000e-19
GCST004131_25	Inflammatory bowel disease	2.000000e-31
GCST004133_79	Ulcerative colitis	5.000000e-65
GCST004521_114	Autism spectrum disorder or schizophrenia	3.000000e-17
GCST004521_117	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_126	Autism spectrum disorder or schizophrenia	2.000000e-10
GCST004521_209	Autism spectrum disorder or schizophrenia	5.000000e-16
GCST004521_211	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_213	Autism spectrum disorder or schizophrenia	5.000000e-13
GCST004521_265	Autism spectrum disorder or schizophrenia	7.000000e-14
GCST004521_27	Autism spectrum disorder or schizophrenia	1.000000e-09
GCST004521_3	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_70	Autism spectrum disorder or schizophrenia	8.000000e-20
GCST004521_81	Autism spectrum disorder or schizophrenia	1.000000e-14
GCST004833_1	Cervical cancer	2.000000e-13
GCST005212_38	Asthma	9.000000e-12
GCST006862_19	Asthma	3.000000e-10
GCST008916_111	Asthma	2.000000e-14
GCST008916_114	Asthma	1.000000e-09
GCST008916_30	Asthma	1.000000e-09
GCST008917_2	Asthma (childhood onset)	4.000000e-07
GCST008921_1	Asthma and major depressive disorder	2.000000e-16
GCST010725_43	Malaria	5.000000e-07
GCST010725_62	Malaria	3.000000e-06
GCST90002388_76	Lymphocyte count	1.000000e-15

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004587	lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Folic Acid	decreases expression	1

Clinical trials (associated diseases)

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