MDH1B

Summary

MDH1B (malate dehydrogenase 1B, HGNC:17836) is a protein-coding gene on chromosome 2q33.3, encoding Putative malate dehydrogenase 1B (Q5I0G3).

Predicted to enable L-malate dehydrogenase (NAD+) activity. Predicted to be involved in NADH metabolic process; dicarboxylic acid metabolic process; and tricarboxylic acid cycle.

Source: NCBI Gene 130752 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 88 total
• MANE Select transcript: NM_001039845

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17836
Approved symbol	MDH1B
Name	malate dehydrogenase 1B
Location	2q33.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25341, RP11-95H11
Ensembl gene	ENSG00000138400
Ensembl biotype	protein_coding
Entrez	130752

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000374412, ENST00000432911, ENST00000436472, ENST00000449792, ENST00000454776, ENST00000471988

RefSeq mRNA: 6 — MANE Select: NM_001039845 NM_001039845, NM_001282940, NM_001330223, NM_001330224, NM_001330225, NM_001330226

CCDS: CCDS33365, CCDS63102, CCDS82561

Canonical transcript exons

ENST00000374412 — 12 exons

Exon	Start	End
ENSE00001463449	206737763	206738511
ENSE00001463455	206750934	206751075
ENSE00001463456	206755009	206755505
ENSE00001803010	206765250	206765328
ENSE00003460330	206739593	206739661
ENSE00003466545	206757237	206757371
ENSE00003559813	206746287	206746426
ENSE00003564194	206760901	206761013
ENSE00003567346	206749020	206749183
ENSE00003567562	206756898	206757040
ENSE00003574442	206745622	206745673
ENSE00003687005	206741054	206741104

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 97.72.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6786 / max 67.9668, expressed in 684 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
33362	1.0693	509
33363	0.6093	265

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	97.72	gold quality
right uterine tube	UBERON:0001302	96.81	gold quality
bronchus	UBERON:0002185	96.34	gold quality
oviduct epithelium	UBERON:0004804	95.65	gold quality
sperm	CL:0000019	91.78	gold quality
mucosa of paranasal sinus	UBERON:0005030	88.57	gold quality
left testis	UBERON:0004533	87.45	gold quality
right testis	UBERON:0004534	86.50	gold quality
testis	UBERON:0000473	86.35	gold quality
fallopian tube	UBERON:0003889	86.05	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	85.81	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.48	gold quality
pituitary gland	UBERON:0000007	83.86	gold quality
epithelium of nasopharynx	UBERON:0001951	83.33	gold quality
adenohypophysis	UBERON:0002196	83.06	gold quality
adult organism	UBERON:0007023	83.06	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.45	gold quality
pancreatic ductal cell	CL:0002079	79.40	silver quality
left lobe of thyroid gland	UBERON:0001120	78.10	gold quality
thyroid gland	UBERON:0002046	77.63	gold quality
metanephros cortex	UBERON:0010533	77.55	gold quality
right lobe of thyroid gland	UBERON:0001119	77.27	gold quality
epithelial cell of pancreas	CL:0000083	77.22	gold quality
caput epididymis	UBERON:0004358	74.10	gold quality
caudate nucleus	UBERON:0001873	73.86	gold quality
nasal cavity epithelium	UBERON:0005384	73.18	silver quality
nucleus accumbens	UBERON:0001882	72.76	gold quality
prefrontal cortex	UBERON:0000451	72.61	gold quality
ventricular zone	UBERON:0003053	72.34	gold quality
metanephros	UBERON:0000081	72.30	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.68
E-GEOD-124858	no	52.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting MDH1B, 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-190A-3P	100.00	80.35	5520
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-6715B-5P	99.64	69.63	1420
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-4269	99.55	69.89	1373
HSA-MIR-549A-3P	99.54	68.17	825
HSA-MIR-888-3P	99.53	69.77	1057

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	mdh1b	ENSDARG00000018008
mus_musculus	Mdh1b	ENSMUSG00000025963
rattus_norvegicus	Mdh1b	ENSRNOG00000012891
drosophila_melanogaster	Mdh1	FBGN0262782
caenorhabditis_elegans		WBGENE00018491

Paralogs (1): MDH1 (ENSG00000014641)

Protein

Protein identifiers

Putative malate dehydrogenase 1B — Q5I0G3 (reviewed: Q5I0G3)

All UniProt accessions (3): B4DY40, C9JER5, Q5I0G3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the LDH/MDH superfamily. MDH type 2 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5I0G3-1	1	yes
Q5I0G3-2	2
Q5I0G3-3	3

RefSeq proteins (6): NP_001034934, NP_001269869, NP_001317152, NP_001317153, NP_001317154, NP_001317155 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010945	Malate_DH_type2	Family
IPR015955	Lactate_DH/Glyco_Ohase_4_C	Homologous_superfamily
IPR022383	Lactate/malate_DH_C	Domain
IPR036291	NAD(P)-bd_dom_sf	Homologous_superfamily

Pfam: PF02866

UniProt features (8 total): splice variant 3, sequence variant 3, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5I0G3-F1	86.46	0.71

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 81 (showing top): GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN, GOBP_OXALOACETATE_METABOLIC_PROCESS, GOBP_NADPLUS_METABOLIC_PROCESS, GOBP_DICARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_CH_OH_GROUP_OF_DONORS, GOBP_CELLULAR_RESPIRATION, GOBP_PURINE_CONTAINING_COMPOUND_METABOLIC_PROCESS, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, RFX1_01, DODD_NASOPHARYNGEAL_CARCINOMA_DN

GO Biological Process (4): tricarboxylic acid cycle (GO:0006099), oxaloacetate metabolic process (GO:0006107), malate metabolic process (GO:0006108), obsolete NADH metabolic process (GO:0006734)

GO Molecular Function (5): L-malate dehydrogenase (NAD+) activity (GO:0030060), catalytic activity (GO:0003824), oxidoreductase activity (GO:0016491), malate dehydrogenase activity (GO:0016615), oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
dicarboxylic acid metabolic process	2
oxidoreductase activity, acting on CH-OH group of donors	2
aerobic respiration	1
primary metabolic process	1
malate dehydrogenase activity	1
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	1
molecular_function	1
catalytic activity	1

Protein interactions and networks

STRING

3115 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MDH1B	TTC16	Q8NEE8	574
MDH1B	OGDH	Q02218	533
MDH1B	PKLR	P11973	512
MDH1B	OGDHL	Q9ULD0	502
MDH1B	FBP1	P09467	487
MDH1B	ACO2	Q99798	481
MDH1B	RBKS	Q9H477	481
MDH1B	PGAM2	P15259	478
MDH1B	PDHB	P11177	476
MDH1B	IDH3A	P50213	472
MDH1B	MDH2	P40926	472
MDH1B	IDH2	P48735	472
MDH1B	ACO1	P21399	471
MDH1B	DLD	P09622	467
MDH1B	FH	P07954	462

IntAct

3 interactions, top by confidence:

A	B	Type	Score
EPHA3	FHAD1	psi-mi:“MI:0914”(association)	0.350
STYK1	MYO1C	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): MDH1B (Affinity Capture-MS), MDH1B (Affinity Capture-MS)

ESM2 similar proteins: A1KXW8, A6QL50, E1BGQ2, H0Y354, O94955, P47224, Q08326, Q0IIH8, Q1JQA1, Q1RMS8, Q1RMZ1, Q2TBU5, Q3T1H6, Q4R372, Q4R528, Q4R9C4, Q5F480, Q5F4A1, Q5I0G3, Q5RCQ0, Q5RFG8, Q5TFE4, Q5TYM5, Q641X7, Q6L9T8, Q6PIP5, Q7L622, Q7Z6J8, Q7ZX59, Q86X60, Q8BFZ8, Q8BKW4, Q8BM85, Q8BX13, Q8CEL2, Q8N5C7, Q8N635, Q8NHU2, Q8TCF1, Q8TCJ0

Diamond homologs: A3KMX7, Q08BZ4, Q5F204, Q5I0G3, Q8T773, A1W9K7, A4FFX3, A5IEF4, B0SF41, B0SN74, B9MBP0, C1B155, P15719, P37229, Q0S365, Q1AWH4, Q47TT4, Q5WU94, Q5X2T6, Q5ZT13, Q82HS2, Q8PNP8, Q9RXI8, F1C7I4, A0PVV1, A0QCI6, B2HRH5, B2UKY5, O24047, O48902, O48905, O88989, P11708, P21528, P40925, P57106, P61976, P93819, Q08062, Q0RE66

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2013 predictions. Top by Δscore:

Variant	Effect	Δscore
2:206749180:CTCA:C	acceptor_gain	1.0000
2:206757227:A:C	donor_gain	1.0000
2:206739662:C:CC	acceptor_gain	0.9900
2:206741053:CCAT:C	donor_gain	0.9900
2:206746280:ACATT:A	donor_loss	0.9900
2:206746281:CATTA:C	donor_loss	0.9900
2:206746282:ATTAC:A	donor_loss	0.9900
2:206746283:TTA:T	donor_loss	0.9900
2:206746284:TACCT:T	donor_loss	0.9900
2:206746285:A:G	donor_loss	0.9900
2:206746286:C:CA	donor_loss	0.9900
2:206746287:C:G	donor_loss	0.9900
2:206746422:CTGGC:C	acceptor_gain	0.9900
2:206746423:TGGCC:T	acceptor_loss	0.9900
2:206746424:GGCCT:G	acceptor_loss	0.9900
2:206746425:GCCTG:G	acceptor_loss	0.9900
2:206746426:CCTGC:C	acceptor_loss	0.9900
2:206746427:C:CC	acceptor_gain	0.9900
2:206746427:CTGC:C	acceptor_loss	0.9900
2:206746428:T:A	acceptor_loss	0.9900
2:206749182:CA:C	acceptor_gain	0.9900
2:206749184:C:CC	acceptor_gain	0.9900
2:206755007:A:AC	donor_gain	0.9900
2:206755008:C:CC	donor_gain	0.9900
2:206755257:T:TA	donor_gain	0.9900
2:206755504:CA:C	acceptor_gain	0.9900
2:206755506:C:CC	acceptor_gain	0.9900
2:206756946:T:TA	donor_gain	0.9900
2:206757036:TAAAG:T	acceptor_gain	0.9900
2:206757041:C:CC	acceptor_gain	0.9900

AlphaMissense

3415 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:206751055:A:G	W311R	0.985
2:206751055:A:T	W311R	0.985
2:206751051:C:A	G312V	0.983
2:206765250:C:G	G8R	0.983
2:206755133:G:C	N262K	0.982
2:206755133:G:T	N262K	0.982
2:206757253:A:G	F85S	0.981
2:206757311:A:G	W66R	0.981
2:206757311:A:T	W66R	0.981
2:206757252:G:C	F85L	0.977
2:206757252:G:T	F85L	0.977
2:206757254:A:G	F85L	0.977
2:206760962:A:G	L25S	0.977
2:206749024:A:C	S404R	0.976
2:206749024:A:T	S404R	0.976
2:206749026:T:G	S404R	0.976
2:206751052:C:G	G312R	0.976
2:206755035:G:T	A295D	0.976
2:206755036:C:G	A295P	0.975
2:206757338:A:G	W57R	0.974
2:206757338:A:T	W57R	0.974
2:206760972:C:G	A22P	0.974
2:206760940:A:C	F32L	0.972
2:206760940:A:T	F32L	0.972
2:206760942:A:G	F32L	0.972
2:206749082:A:G	L385P	0.971
2:206755479:A:G	L147P	0.971
2:206749074:A:G	W388R	0.969
2:206749074:A:T	W388R	0.969
2:206757242:C:G	A89P	0.968

dbSNP variants (sampled 300 via entrez): RS1000004909 (2:206744510 C>T), RS1000290596 (2:206745278 T>C), RS1000365316 (2:206751510 A>G), RS1000369963 (2:206758964 T>G), RS1000372909 (2:206758148 A>G), RS1000390414 (2:206757968 A>C), RS1000396391 (2:206751793 T>G), RS1000593048 (2:206739028 G>A), RS1000644193 (2:206745733 T>A,C), RS1000704384 (2:206757441 T>C,G), RS1000732735 (2:206750247 T>C), RS1000762814 (2:206757685 G>C), RS1001102986 (2:206750064 T>C), RS1001213818 (2:206764238 C>T), RS1001382041 (2:206738265 G>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

4 associations (top):

Study	Trait	p-value
GCST005951_45	Body mass index	1.000000e-09
GCST009391_420	Metabolite levels	3.000000e-06
GCST009391_906	Metabolite levels	9.000000e-07
GCST009391_923	Metabolite levels	3.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0010388	phosphatidylcholine 38:6 measurement
EFO:0010442	triacylglycerol 58:8 measurement
EFO:0010443	triacylglycerol 58:9 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
Gold	decreases expression, affects binding	2
methylmercuric chloride	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
CGP 52608	increases reaction, affects binding	1
abrine	decreases expression	1
jinfukang	increases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Polyethyleneimine	affects binding, decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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