BKGD

Summary

BKGD (beta-keto-L-gulonate decarboxylase, HGNC:30204) is a protein-coding gene on chromosome 11q21, encoding Beta-keto L-gulonate decarboxylase (Q9H0W9). Catalyzes the decarboxylation of 3-dehydro-L-gulonate to produce L-xylulose, used in the pentose pathway.

Enables hydrolase activity, acting on ester bonds and zinc ion binding activity. Located in nuclear body.

Source: NCBI Gene 28970 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 19 total — 1 likely-pathogenic
• MANE Select transcript: NM_001286069

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30204
Approved symbol	BKGD
Name	beta-keto-L-gulonate decarboxylase
Location	11q21
Locus type	gene with protein product
Status	Approved
Aliases	PTD012, MEEP
Ensembl gene	ENSG00000182919
Ensembl biotype	protein_coding
OMIM	615810
Entrez	28970

Gene structure

Transcript identifiers

Ensembl transcripts: 73 — 72 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000331239, ENST00000354421, ENST00000526335, ENST00000527003, ENST00000527363, ENST00000528099, ENST00000528288, ENST00000530279, ENST00000530620, ENST00000531516, ENST00000531650, ENST00000533154, ENST00000533585, ENST00000540113, ENST00000617482, ENST00000906870, ENST00000906871, ENST00000906872, ENST00000906873, ENST00000906874, ENST00000906875, ENST00000906876, ENST00000906877, ENST00000906878, ENST00000906879, ENST00000906880, ENST00000906881, ENST00000906882, ENST00000906883, ENST00000906884, ENST00000906885, ENST00000906886, ENST00000906887, ENST00000906888, ENST00000906889, ENST00000906890, ENST00000906891, ENST00000906892, ENST00000906893, ENST00000906894, ENST00000906895, ENST00000906896, ENST00000906897, ENST00000906898, ENST00000906899, ENST00000906900, ENST00000906901, ENST00000906902, ENST00000906903, ENST00000906904, ENST00000906905, ENST00000906906, ENST00000906907, ENST00000906908, ENST00000906909, ENST00000906910, ENST00000906911, ENST00000906912, ENST00000906913, ENST00000906914, ENST00000917262, ENST00000917263, ENST00000917264, ENST00000917265, ENST00000917266, ENST00000951671, ENST00000951672, ENST00000951673, ENST00000951674, ENST00000951675, ENST00000951676, ENST00000951677, ENST00000951678

RefSeq mRNA: 16 — MANE Select: NM_001286069 NM_001286067, NM_001286068, NM_001286069, NM_001286070, NM_001286071, NM_001351985, NM_001351986, NM_001351987, NM_001351988, NM_001351989, NM_001351990, NM_001351991, NM_001351992, NM_001351993, NM_001369406, NM_014039

CCDS: CCDS66204, CCDS73365, CCDS73366, CCDS8294

Canonical transcript exons

ENST00000354421 — 9 exons

Exon	Start	End
ENSE00001299034	93755210	93755386
ENSE00001301186	93753936	93754037
ENSE00001301691	93757316	93757465
ENSE00001311195	93753682	93753755
ENSE00001317155	93759742	93759858
ENSE00001412635	93741672	93741728
ENSE00002171678	93761515	93764749
ENSE00003530650	93747297	93747448
ENSE00003586508	93750346	93750444

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 99.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.8654 / max 435.4541, expressed in 1767 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116237	10.7595	1759
116236	1.5078	847
116240	0.3945	30
116239	0.1683	24
116241	0.0134	3
116242	0.0121	4
116238	0.0098	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	99.93	gold quality
renal medulla	UBERON:0000362	98.99	gold quality
adult organism	UBERON:0007023	98.34	gold quality
adult mammalian kidney	UBERON:0000082	98.22	gold quality
ileal mucosa	UBERON:0000331	97.94	gold quality
kidney	UBERON:0002113	97.90	gold quality
jejunal mucosa	UBERON:0000399	97.43	gold quality
liver	UBERON:0002107	96.96	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.23	gold quality
epithelial cell of pancreas	CL:0000083	95.88	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	95.85	gold quality
metanephros	UBERON:0000081	95.80	gold quality
pigmented layer of retina	UBERON:0001782	95.72	gold quality
colonic mucosa	UBERON:0000317	95.65	gold quality
bronchial epithelial cell	CL:0002328	95.64	gold quality
gall bladder	UBERON:0002110	95.54	gold quality
jejunum	UBERON:0002115	95.47	gold quality
right lobe of liver	UBERON:0001114	95.41	gold quality
cortex of kidney	UBERON:0001225	95.38	gold quality
mucosa of sigmoid colon	UBERON:0004993	95.30	gold quality
bronchus	UBERON:0002185	95.08	gold quality
biceps brachii	UBERON:0001507	94.82	gold quality
duodenum	UBERON:0002114	94.59	gold quality
rectum	UBERON:0001052	94.26	gold quality
caput epididymis	UBERON:0004358	94.24	gold quality
lower lobe of lung	UBERON:0008949	94.18	gold quality
metanephros cortex	UBERON:0010533	94.15	gold quality
vastus lateralis	UBERON:0001379	93.98	gold quality
oral cavity	UBERON:0000167	93.87	gold quality
body of pancreas	UBERON:0001150	93.84	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-HCAD-10	yes	38.90
E-ANND-3	yes	17.97
E-GEOD-124858	no	134.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

100 targeting BKGD, 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-5692A	100.00	74.40	6850
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786

Literature-anchored findings (GeneRIF, showing 1)

• C11orf54 promotes DNA repair via blocking CMA-mediated degradation of HIF1A. (PMID:37277441)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	C5H11orf54	ENSDARG00000110147
mus_musculus	4931406C07Rik	ENSMUSG00000031938
rattus_norvegicus	C8h11orf54	ENSRNOG00000010887
drosophila_melanogaster	CG9119	FBGN0035189
drosophila_melanogaster	meep	FBGN0063667
caenorhabditis_elegans		WBGENE00016046

Protein

Protein identifiers

Beta-keto L-gulonate decarboxylase — Q9H0W9 (reviewed: Q9H0W9)

All UniProt accessions (11): A0A024R3B0, A0A087WT99, Q9H0W9, E9PIP1, E9PJU8, E9PLB3, E9PLC5, E9PPB5, E9PQS1, E9PR95, E9PSC3

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the decarboxylation of 3-dehydro-L-gulonate to produce L-xylulose, used in the pentose pathway. Exhibits ester hydrolase activity on p-nitrophenyl acetate, in vitro. Regulates DNA damage and repair by regulating HIF1A degradation via chaperone-mediated autophagy (CMA). Probably non-functional when tested on p-nitrophenyl acetate, in vitro.

Subunit / interactions. Monomer.

Subcellular location. Nucleus. Cytoplasm.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9H0W9-1	1	yes
Q9H0W9-2	2
Q9H0W9-3	3
Q9H0W9-4	4

RefSeq proteins (16): NP_001272996, NP_001272997, NP_001272998, NP_001272999, NP_001273000, NP_001338914, NP_001338915, NP_001338916, NP_001338917, NP_001338918, NP_001338919, NP_001338920, NP_001338921, NP_001338922, NP_001356335, NP_054758 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR015021	C11orf54_DUF1907	Domain

Pfam: PF08925

Catalyzed reactions (Rhea), 1 shown:

• 3-dehydro-L-gulonate + H(+) = L-xylulose + CO2 (RHEA:11084)

UniProt features (44 total): strand 22, helix 7, binding site 3, sequence conflict 3, turn 3, splice variant 3, mutagenesis site 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
1XCR	X-RAY DIFFRACTION	1.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H0W9-F1	97.55	0.98

Functional residue map

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

Ligand- & substrate-binding residues (3): 266; 268; 278

Mutagenesis-validated functional residues (2):

Position	Phenotype
217	abolishes enzyme activity.
263	abolishes enzyme activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 159 (showing top): GOBP_REGULATION_OF_DNA_REPAIR, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOBP_DNA_DAMAGE_RESPONSE, TSENG_IRS1_TARGETS_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_STRESS, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, WENG_POR_TARGETS_LIVER_UP, BURTON_ADIPOGENESIS_6, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN, GOBP_DNA_METABOLIC_PROCESS

GO Biological Process (2): regulation of DNA repair (GO:0006282), DNA damage response (GO:0006974)

GO Molecular Function (5): zinc ion binding (GO:0008270), hydrolase activity, acting on ester bonds (GO:0016788), protein binding (GO:0005515), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear body (GO:0016604), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
DNA repair	1
regulation of DNA metabolic process	1
regulation of cellular response to stress	1
cellular response to stress	1
transition metal ion binding	1
hydrolase activity	1
binding	1
catalytic activity	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
nucleoplasm	1
intracellular membraneless organelle	1
extracellular vesicle	1

Protein interactions and networks

STRING

388 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BKGD	VSTM5	A8MXK1	585
BKGD	CCDC82	Q8N4S0	499
BKGD	SMCO4	Q9NRQ5	490
BKGD	TBC1D22B	Q9NU19	490
BKGD	MED17	Q9NVC6	488
BKGD	URB2	Q14146	480
BKGD	FRMD1	Q8N878	442
BKGD	HEPHL1	Q6MZM0	437
BKGD	TAF1D	Q9H5J8	412
BKGD	HEPH	Q9BQS7	407
BKGD	AMMECR1L	Q6DCA0	397
BKGD	TAF1B	Q53T94	395
BKGD	C8orf89	P0DMQ9	390
BKGD	CEP41	Q9BYV8	377
BKGD	HDHD2	Q9H0R4	370

IntAct

17 interactions, top by confidence:

A	B	Type	Score
ASH2L	KMT2D	psi-mi:“MI:0914”(association)	0.890
VAC14	C11orf54	psi-mi:“MI:0915”(physical association)	0.670
C11orf54	VAC14	psi-mi:“MI:0915”(physical association)	0.670
TRIP13	C11orf54	psi-mi:“MI:0915”(physical association)	0.620
C11orf54	SSX2IP	psi-mi:“MI:0915”(physical association)	0.560
SSX2IP	C11orf54	psi-mi:“MI:0915”(physical association)	0.560
C11orf54	COA7	psi-mi:“MI:0915”(physical association)	0.560
C11orf54	COA7	psi-mi:“MI:0914”(association)	0.560
COL10A1	P4HA2	psi-mi:“MI:0914”(association)	0.350
PEX7	UBA6	psi-mi:“MI:0914”(association)	0.350
VENTX	UBA6	psi-mi:“MI:0914”(association)	0.350

BioGRID (60): VAC14 (Two-hybrid), SSX2IP (Two-hybrid), CCT2 (Affinity Capture-MS), C11orf54 (Two-hybrid), BCAT2 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation), C11orf54 (Co-fractionation)

ESM2 similar proteins: B2S270, O83159, P09810, P11982, P13444, P17290, P17432, P17532, P17752, P20007, P22130, P23225, P40320, P70080, Q03460, Q05893, Q08AW5, Q0DG35, Q0EAB8, Q1LZE8, Q28GJ2, Q2FN14, Q2HJH3, Q2HZ26, Q43155, Q5BKL1, Q5M888, Q5U2Q3, Q69RJ0, Q6DDT1, Q6GME2, Q6NWE0, Q7RVS9, Q7ZXY0, Q8BH04, Q8CGU9, Q8CGV2, Q8IWU9, Q8VHT6, Q91V76

Diamond homologs: Q28GJ2, Q2HJH3, Q5U2Q3, Q6GME2, Q6NWE0, Q91V76, Q9H0W9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	6
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1527656	GRCh37/hg19 11q14.1-21(chr11:84924674-93574799)	Likely pathogenic

SpliceAI

1500 predictions. Top by Δscore:

Variant	Effect	Δscore
11:93747269:T:G	acceptor_gain	1.0000
11:93750143:G:GT	donor_gain	1.0000
11:93750143:G:T	donor_gain	1.0000
11:93750344:A:AG	acceptor_gain	1.0000
11:93750345:G:GA	acceptor_gain	1.0000
11:93750345:GT:G	acceptor_gain	1.0000
11:93750345:GTT:G	acceptor_gain	1.0000
11:93750345:GTTAT:G	acceptor_gain	1.0000
11:93750440:AAAAG:A	donor_loss	1.0000
11:93750442:AAGGT:A	donor_loss	1.0000
11:93750443:AGGTA:A	donor_loss	1.0000
11:93750444:GGT:G	donor_loss	1.0000
11:93750445:G:A	donor_loss	1.0000
11:93750446:T:A	donor_loss	1.0000
11:93753668:T:TA	acceptor_gain	1.0000
11:93753669:G:A	acceptor_gain	1.0000
11:93753677:CTTAG:C	acceptor_loss	1.0000
11:93753678:TTAGG:T	acceptor_loss	1.0000
11:93753679:TAG:T	acceptor_loss	1.0000
11:93753680:A:AG	acceptor_gain	1.0000
11:93753680:A:AT	acceptor_loss	1.0000
11:93753681:G:GG	acceptor_gain	1.0000
11:93753751:AAAAA:A	donor_gain	1.0000
11:93753753:AAA:A	donor_gain	1.0000
11:93753753:AAAG:A	donor_loss	1.0000
11:93753754:AA:A	donor_gain	1.0000
11:93753755:AGTA:A	donor_loss	1.0000
11:93753756:G:GG	donor_gain	1.0000
11:93753756:GTAA:G	donor_loss	1.0000
11:93753930:CTATA:C	acceptor_loss	1.0000

AlphaMissense

2082 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:93761645:G:C	R302P	0.993
11:93757342:A:C	R178S	0.990
11:93757342:A:T	R178S	0.990
11:93757413:G:A	G202E	0.988
11:93755366:A:C	S163R	0.987
11:93755368:T:A	S163R	0.987
11:93755368:T:G	S163R	0.987
11:93750372:T:C	F28L	0.986
11:93750374:T:A	F28L	0.986
11:93750374:T:G	F28L	0.986
11:93755261:A:C	S128R	0.986
11:93755263:T:A	S128R	0.986
11:93755263:T:G	S128R	0.986
11:93757419:G:A	G204E	0.986
11:93761584:G:C	D282H	0.985
11:93757341:G:C	R178T	0.984
11:93755358:T:C	L160P	0.983
11:93759829:T:C	C249R	0.983
11:93753715:G:A	G63E	0.982
11:93761538:C:A	H266Q	0.982
11:93761538:C:G	H266Q	0.982
11:93761608:T:C	Y290H	0.982
11:93757418:G:A	G204R	0.981
11:93757418:G:C	G204R	0.981
11:93761537:A:C	H266P	0.981
11:93757422:G:A	G205D	0.979
11:93761615:G:A	G292E	0.979
11:93761630:C:A	A297E	0.978
11:93753994:G:A	G96E	0.977
11:93761536:C:G	H266D	0.977

dbSNP variants (sampled 300 via entrez): RS1000002165 (11:93741772 A>C), RS1000096681 (11:93742040 G>T), RS1000181338 (11:93750637 G>A), RS1000291845 (11:93745995 C>T), RS1000311746 (11:93740883 G>C,T), RS1000618151 (11:93741168 G>A), RS1000684590 (11:93752813 A>G), RS1000698233 (11:93758877 G>C), RS1000822011 (11:93753037 G>A,T), RS1000962418 (11:93741170 G>A), RS1001209838 (11:93746816 A>G), RS1001284265 (11:93751927 A>G), RS1001284923 (11:93762061 A>G), RS1001566894 (11:93759536 A>G), RS1001577319 (11:93753315 C>A,T)

Disease associations

OMIM: gene MIM:615810 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	4
bisphenol A	increases expression, affects cotreatment, decreases methylation, increases methylation	2
Formaldehyde	decreases expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	2
Cyclosporine	decreases expression	2
Aflatoxin B1	decreases expression	2
Cadmium Chloride	increases expression	2
Particulate Matter	decreases expression, increases abundance	2
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
methyleugenol	decreases expression	1
glycidyl methacrylate	decreases expression	1
beta-lapachone	decreases expression	1
potassium chromate(VI)	increases expression	1
cupric chloride	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
NSC 689534	affects binding, increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Ascorbic Acid	affects cotreatment, decreases expression	1
Benzo(a)pyrene	decreases expression	1
Calcitriol	increases expression	1
Cisplatin	increases expression	1
Copper	affects binding, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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