AiPD: Autoinhibited Protein Database

Q9Y6M9

Gene name	NDUFB9 (LYRM3, UQOR22)
Protein name	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Names	Complex I-B22, CI-B22, LYR motif-containing protein 3, NADH-ubiquinone oxidoreductase B22 subunit
Species	Homo sapiens (Human)
KEGG Pathway	hsa:4715
EC number
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

101-179 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

101-179 (Predicted disordered autoinhibitory region)

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Yeon JH et al. (2016) "Systems-wide Identification of cis-Regulatory Elements in Proteins", Cell Systems, 2, 89-100

Autoinhibited structure

Activated structure

5 structures for Q9Y6M9

Entry ID	Method	Resolution	Chain	Position	Source
5XTC	EM	370 A	p	8-179	PDB
5XTD	EM	370 A	p	8-179	PDB
5XTH	EM	390 A	p	8-179	PDB
5XTI	EM	1740 A	Bp/p	8-179	PDB
AF-Q9Y6M9-F1	Predicted				AlphaFoldDB

171 variants for Q9Y6M9

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
CA4871488 RCV000055653 VAR_081460 rs776388520	64	L>P	Mitochondrial complex 1 deficiency, nuclear type 24 MC1DN24 [ClinVar, UniProt]	Yes	ClinGen ClinVar UniProt ExAC TOPMed dbSNP gnomAD
RCV002222504 RCV000438795 rs369824948	1	M>V		No	ClinVar dbSNP
rs576180546 CA4871427	2	A>T		No	ClinGen 1000Genomes ExAC gnomAD
CA4871428 rs754264800	2	A>V	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
CA4871431 rs753001361	4	L>W		No	ClinGen ExAC TOPMed gnomAD
CA4871434 CA4871433 rs780702672	7	G>R		No	ClinGen ExAC gnomAD
rs755557988 CA4871435	8	P>H		No	ClinGen ExAC TOPMed gnomAD
rs755557988 RCV002054331 CA324363 RCV000199816	8	P>L		No	ClinGen ClinVar ExAC TOPMed dbSNP gnomAD
rs747887062 CA4871438	9	Y>C		No	ClinGen ExAC gnomAD
rs747887062 CA4871439	9	Y>F		No	ClinGen ExAC gnomAD
rs748125978 CA4871437	9	Y>H		No	ClinGen ExAC TOPMed gnomAD
CA185324286 rs747887062	9	Y>S		No	ClinGen ExAC gnomAD
rs1458680483 CA372169872	10	L>R		No	ClinGen TOPMed gnomAD
CA4871441 rs148083715	10	L>V		No	ClinGen ESP ExAC TOPMed gnomAD
rs775505346 CA185324311	11	T>I		No	ClinGen gnomAD
CA4871442 rs771085676	12	H>L		No	ClinGen ExAC TOPMed gnomAD
CA372169920 rs1471245383	12	H>Q		No	ClinGen gnomAD
rs1181119187 CA372169903	12	H>Y		No	ClinGen gnomAD
rs1161517938 CA372169945	13	Q>R		No	ClinGen TOPMed gnomAD
CA372169964 rs1384366039	14	Q>P		No	ClinGen gnomAD
CA372170024 rs1425275407	17	L>S		No	ClinGen gnomAD
CA372170018 rs1586706858	17	L>V		No	ClinGen Ensembl
CA372170072 rs375156568	20	Y>C		No	ClinGen TOPMed
CA185324317 rs375156568	20	Y>F		No	ClinGen TOPMed
rs1170091504 CA372170092	21	K>N		No	ClinGen TOPMed
CA372170102 rs1390326483	22	R>P		No	ClinGen TOPMed gnomAD
CA372170101 rs1390326483	22	R>Q		No	ClinGen TOPMed gnomAD
rs759625380 CA4871444	22	R>W		No	ClinGen ExAC gnomAD
rs753267338 CA4871446	25	R>C		No	ClinGen ExAC gnomAD
CA4871447 rs763215805	25	R>H		No	ClinGen ExAC gnomAD
CA372170138 rs763215805	25	R>L		No	ClinGen ExAC gnomAD
CA185324355 rs987331242	27	L>V		No	ClinGen Ensembl
CA4871451 rs200160068	28	E>G		No	ClinGen ExAC gnomAD
CA4871450 rs755752997	28	E>Q		No	ClinGen ExAC TOPMed gnomAD
rs1376173919 CA372170219	30	W>C		No	ClinGen gnomAD
rs1586707053 CA372170226	31	C>G		No	ClinGen Ensembl
rs1477840167 CA372170240	32	V>I		No	ClinGen gnomAD
CA4871472 rs753614800	36	K>T		No	ClinGen ExAC gnomAD
CA4871474 rs778604920	37	Y>*		No	ClinGen ExAC TOPMed gnomAD
CA4871473 RCV000522472 rs140417066	37	Y>H		No	ClinGen ClinVar 1000Genomes ESP ExAC TOPMed dbSNP gnomAD
rs752176530 CA4871475 COSM245982	38	R>*	prostate [Cosmic]	No	ClinGen cosmic curated ExAC TOPMed gnomAD
CA372172097 rs1410934897	38	R>Q		No	ClinGen TOPMed
rs1586713497 CA372172142	40	F>L		No	ClinGen Ensembl
rs777584999 CA4871477	41	A>S		No	ClinGen ExAC gnomAD
rs1342883348 CA372172191	42	C>G		No	ClinGen TOPMed gnomAD
CA372172193 rs1342883348	42	C>R		No	ClinGen TOPMed gnomAD
CA372172218 rs1586713513	43	L>F		No	ClinGen Ensembl
CA4871478 rs200794750	44	M>L		No	ClinGen ESP ExAC TOPMed gnomAD
rs1563706936 CA372172273	46	A>G		No	ClinGen Ensembl
CA185326836 rs770697169	46	A>S		No	ClinGen ExAC TOPMed gnomAD
CA4871479 rs770697169	46	A>T		No	ClinGen ExAC TOPMed gnomAD
rs142723791 RCV000971286 CA4871480	47	R>L		No	ClinGen ClinVar 1000Genomes ESP ExAC TOPMed dbSNP gnomAD
CA372172288 rs142723791	47	R>Q		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA372172285 rs1212484074	47	R>W		No	ClinGen TOPMed gnomAD
COSM1488987 rs1205448869 CA372172386	51	H>R	Variant assessed as Somatic; 0.0 impact. breast [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA gnomAD
rs746138914 CA4871481	51	H>Y		No	ClinGen ExAC gnomAD
rs769836178 CA4871482	52	K>E		No	ClinGen ExAC TOPMed gnomAD
CA185326851 rs923540282	52	K>R		No	ClinGen Ensembl
TCGA novel	52	K>T	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs775508441 CA4871483	53	N>H		No	ClinGen ExAC TOPMed gnomAD
CA4871484 rs138066988	54	E>V		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA4871485 rs769151839	56	D>G		No	ClinGen ExAC TOPMed gnomAD
rs1450763254 CA372172469	56	D>N		No	ClinGen TOPMed gnomAD
CA4871486 rs774728394	57	M>I	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
rs1586713582 CA372172527	58	A>T		No	ClinGen Ensembl
CA372172534 COSM1454730 rs1156454853	58	A>V	Variant assessed as Somatic; 0.0 impact. large_intestine [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA TOPMed gnomAD
rs1322011633 CA372172586	60	A>V		No	ClinGen TOPMed
rs762235847 CA323309	61	T>I		No	ClinGen ExAC TOPMed gnomAD
rs762235847 CA4871487	61	T>S		No	ClinGen ExAC TOPMed gnomAD
CA372172669 rs1586713598	65	K>R		No	ClinGen Ensembl
rs1363079117 CA372172682	66	E>*		No	ClinGen gnomAD
CA372172689 rs1363079117	66	E>Q		No	ClinGen gnomAD
rs200765174 CA4871489	67	A>G		No	ClinGen 1000Genomes ExAC gnomAD
CA4871490 rs200765174	67	A>V		No	ClinGen 1000Genomes ExAC gnomAD
CA372172737 rs1220973355	68	E>D		No	ClinGen gnomAD
CA4871491 rs757850670	68	E>K		No	ClinGen ExAC TOPMed gnomAD
CA4871492 rs764088124	69	E>K		No	ClinGen ExAC TOPMed gnomAD
CA372172768 rs1316495306	70	E>G		No	ClinGen gnomAD
CA372172763 rs1563707040	70	E>Q		No	ClinGen Ensembl
rs1287891555 CA372172809	71	F>L		No	ClinGen gnomAD
CA185326886 rs886513928 COSM1286542	72	W>R	autonomic_ganglia Variant assessed as Somatic; impact. [Cosmic, NCI-TCGA]	No	ClinGen cosmic curated Ensembl NCI-TCGA
rs1586713668 CA372172852	73	Y>*		No	ClinGen Ensembl
CA185326889 rs776041417	73	Y>C		No	ClinGen Ensembl
CA372172836 rs1586713656	73	Y>H		No	ClinGen Ensembl
CA372172843 rs776041417	73	Y>S		No	ClinGen Ensembl
CA4871494 rs199940282	74	R>C	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen 1000Genomes ExAC NCI-TCGA gnomAD
rs781006386 CA4871495	74	R>H		No	ClinGen ExAC TOPMed gnomAD
CA372172855 rs199940282	74	R>S		No	ClinGen 1000Genomes ExAC gnomAD
rs1390486233 CA372173089	83	P>R		No	ClinGen gnomAD
rs1028737029 CA185326904	84	D>G		No	ClinGen TOPMed gnomAD
CA4871499 rs749327318	86	P>S		No	ClinGen ExAC gnomAD
CA4871501 rs774911600	89	T>I		No	ClinGen ExAC TOPMed gnomAD
rs1350921819 CA372173271	90	S>F		No	ClinGen gnomAD
rs748640862 CA4871502	91	Y>C		No	ClinGen ExAC TOPMed gnomAD
CA372173273 rs1438715159	91	Y>H		No	ClinGen gnomAD
CA372173300 rs1372954937	92	E>*		No	ClinGen gnomAD
rs1447783213 CA372173351	93	R>S		No	ClinGen gnomAD
rs979268243 CA185326915	94	Y>*		No	ClinGen TOPMed
rs1563707144 CA585276154	94	Y>*		No	ClinGen Ensembl
CA4871503 rs548548059	94	Y>H		No	ClinGen 1000Genomes ExAC
CA372173403 rs1586713807	95	D>E		No	ClinGen Ensembl
CA4871504 rs773659445	95	D>N		No	ClinGen ExAC TOPMed gnomAD
rs761131395 CA4871505	96	C>F		No	ClinGen ExAC TOPMed gnomAD
rs761131395 CA372173426	96	C>Y		No	ClinGen ExAC TOPMed gnomAD
CA372173450 rs1586713824	97	Y>C		No	ClinGen Ensembl
CA372173442 rs1292438365	97	Y>H		No	ClinGen gnomAD
rs760453137 CA4871532	99	V>A		No	ClinGen ExAC gnomAD
CA185328405 rs897454536	100	P>S		No	ClinGen Ensembl
CA372174921 rs1563708827	101	E>V		No	ClinGen Ensembl
CA4871535 rs372734232	102	W>*		No	ClinGen ESP ExAC TOPMed gnomAD
CA4871534 rs372734232 CA185328414	102	W>C		No	ClinGen ESP ExAC TOPMed gnomAD
rs757935794 CA4871536	103	C>G		No	ClinGen ExAC TOPMed gnomAD
CA372174995 rs1334625667	105	D>G		No	ClinGen gnomAD
rs752754525 CA4871538	112	K>R		No	ClinGen ExAC gnomAD
CA4871537 rs752754525	112	K>T		No	ClinGen ExAC gnomAD
rs779578444 CA4871541	114	M>L		No	ClinGen ExAC TOPMed gnomAD
rs552211537 CA185328431	114	M>T		No	ClinGen Ensembl
rs779578444 CA4871540	114	M>V		No	ClinGen ExAC TOPMed gnomAD
rs781372333 CA4871542 RCV000488057	116	P>L		No	ClinGen ClinVar ExAC TOPMed dbSNP gnomAD
CA4871543 rs746268822	117	D>H		No	ClinGen ExAC gnomAD
rs1367043692 CA372175234	121	K>R		No	ClinGen TOPMed
CA372175242 rs1167377589	122	R>G		No	ClinGen TOPMed
CA4871544 rs768136192	124	Q>E		No	ClinGen ExAC gnomAD
rs774058277 CA4871545	125	W>G		No	ClinGen ExAC gnomAD
rs1200656809 CA372175347	128	L>P		No	ClinGen gnomAD
CA4871546 rs761311925	128	L>V		No	ClinGen ExAC gnomAD
CA372175358 rs141620081	129	R>L		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA4871547 rs141620081	129	R>Q		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs1444524278 CA372175443	135	R>*	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen NCI-TCGA TOPMed gnomAD
rs1444524278 CA372175441	135	R>G		No	ClinGen TOPMed gnomAD
CA4871549 rs773114715	135	R>L		No	ClinGen ExAC gnomAD
CA4871548 rs773114715	135	R>Q		No	ClinGen ExAC gnomAD
rs1454674969 CA372175453	136	E>Q		No	ClinGen gnomAD
CA372177213 rs1188858737	141	Q>R		No	ClinGen TOPMed
CA4871591 rs769883777	144	T>M		No	ClinGen ExAC TOPMed gnomAD
CA185329532 rs10195	146	P>A		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA292474 rs10195 RCV000127134 VAR_014484 RCV000677050	146	P>S		No	ClinGen ClinVar UniProt 1000Genomes ESP ExAC TOPMed dbSNP gnomAD
rs764345953 CA372177306	147	G>A		No	ClinGen ExAC gnomAD
rs764345953 CA4871593	147	G>D		No	ClinGen ExAC gnomAD
CA185329547 rs917197244	150	L>I		No	ClinGen Ensembl
rs774703197 CA4871594	150	L>S		No	ClinGen ExAC TOPMed gnomAD
CA372177381 rs1170688220	153	A>T		No	ClinGen gnomAD
rs945856680 CA185329552	153	A>V		No	ClinGen Ensembl
rs925703332 CA185329558	155	P>T		No	ClinGen gnomAD
CA372177424 rs1586721170	156	P>H		No	ClinGen Ensembl
CA372177432 rs1401904143	157	A>P		No	ClinGen gnomAD
rs148402231 CA4871596	158	R>*		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs148402231 CA320693 RCV000677051	158	R>G		No	ClinGen ClinVar 1000Genomes ESP ExAC TOPMed dbSNP gnomAD
TCGA novel	158	R>Q	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA16603357 RCV000430968 CA4871598 rs774020236	159	K>N		No	ClinGen ClinVar ExAC TOPMed dbSNP gnomAD
CA185329565 rs1047348445	159	K>R		No	ClinGen TOPMed
CA4871599 rs754130870	162	D>E		No	ClinGen ExAC TOPMed gnomAD
rs1168981366 CA372177482	162	D>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen Ensembl NCI-TCGA
TCGA novel	164	P>S	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1586721284 CA372177516	166	L>V		No	ClinGen Ensembl
CA372177528 rs1164291466	167	W>*		No	ClinGen TOPMed
CA372177522 rs1378866096	167	W>G		No	ClinGen gnomAD
CA372177533 rs1470115457	168	W>S		No	ClinGen TOPMed
TCGA novel	170	I>S	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA372177582 rs1255237756	172	T>I		No	ClinGen gnomAD
CA372177581 rs1255237756	172	T>S		No	ClinGen gnomAD
CA4871603 rs373484388	174	P>L		No	ClinGen ESP ExAC TOPMed gnomAD
CA372177606 rs1483466002	174	P>T		No	ClinGen gnomAD
rs745392030 CA372177617	175	R>G		No	ClinGen ExAC TOPMed gnomAD
TCGA novel	175	R>P	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA4871606 rs141607351	175	R>Q		No	ClinGen ESP ExAC TOPMed gnomAD
COSM749441 rs745392030 CA4871605	175	R>W	lung Variant assessed as Somatic; 9.24e-05 impact. [Cosmic, NCI-TCGA]	No	ClinGen cosmic curated ExAC NCI-TCGA TOPMed gnomAD
rs780144498 RCV000726624 RCV000344205 CA4871607	177	R>Q		No	ClinGen ClinVar ExAC dbSNP gnomAD
rs1425123491 CA372177643	177	R>W		No	ClinGen TOPMed gnomAD
CA4871608 rs200683472	179	M>T		No	ClinGen ESP ExAC TOPMed gnomAD
CA372177700 rs1377795411	180	M>W		No	ClinGen gnomAD

1 associated diseases with Q9Y6M9

[MIM: 618245]: Mitochondrial complex I deficiency, nuclear type 24 (MC1DN24)

A form of mitochondrial complex I deficiency, the most common biochemical signature of mitochondrial disorders, a group of highly heterogeneous conditions characterized by defective oxidative phosphorylation, which collectively affects 1 in 5-10000 live births. Clinical disorders have variable severity, ranging from lethal neonatal disease to adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some forms of Parkinson disease. MC1DN24 transmission pattern is consistent with autosomal recessive inheritance. {ECO:0000269|PubMed:22200994}. Note=The disease is caused by variants affecting the gene represented in this entry.

Without disease ID

A form of mitochondrial complex I deficiency, the most common biochemical signature of mitochondrial disorders, a group of highly heterogeneous conditions characterized by defective oxidative phosphorylation, which collectively affects 1 in 5-10000 live births. Clinical disorders have variable severity, ranging from lethal neonatal disease to adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some forms of Parkinson disease. MC1DN24 transmission pattern is consistent with autosomal recessive inheritance. {ECO:0000269|PubMed:22200994}. Note=The disease is caused by variants affecting the gene represented in this entry.

2 regional properties for Q9Y6M9

Type	Name	Position	InterPro Accession
domain	Complex 1 LYR protein domain	14 - 71	IPR008011
domain	NDUFB9, LYR domain	12 - 88	IPR045292

Functions

		Description
EC Number
Subcellular Localization	Mitochondrion inner membrane ; Peripheral membrane protein ; Matrix side
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

3 GO annotations of cellular component

Name	Definition
mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
mitochondrial respiratory chain complex I	A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone.
mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

1 GO annotations of molecular function

Name	Definition
NADH dehydrogenase (ubiquinone) activity	Catalysis of the reaction: NADH + ubiquinone + 5 H(+)(in) <=> NAD(+) + ubiquinol + 4 H(+)(out).

5 GO annotations of biological process

Name	Definition
aerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
mitochondrial electron transport, NADH to ubiquinone	The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation.
mitochondrial respiratory chain complex I assembly	The aggregation, arrangement and bonding together of a set of components to form mitochondrial respiratory chain complex I.
proton motive force-driven mitochondrial ATP synthesis	The transport of protons across a mitochondrial membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
sensory perception of sound	The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.

2 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
Q02369	NDUFB9	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	Bos taurus (Bovine)	PR
Q0MQF0	NDUFB9	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	Pan troglodytes (Chimpanzee)	PR

10	20	30	40	50	60
MAFLASGPYL	THQQKVLRLY	KRALRHLESW	CVQRDKYRYF	ACLMRARFEE	HKNEKDMAKA
70	80	90	100	110	120
TQLLKEAEEE	FWYRQHPQPY	IFPDSPGGTS	YERYDCYKVP	EWCLDDWHPS	EKAMYPDYFA
130	140	150	160	170
KREQWKKLRR	ESWEREVKQL	QEETPPGGPL	TEALPPARKE	GDLPPLWWYI	VTRPRERPM