SCCPDH

Summary

SCCPDH (saccharopine dehydrogenase (putative), HGNC:24275) is a protein-coding gene on chromosome 1q44, encoding Saccharopine dehydrogenase-like oxidoreductase (Q8NBX0).

Predicted to enable oxidoreductase activity. Predicted to be involved in glycolipid biosynthetic process. Located in lipid droplet and midbody.

Source: NCBI Gene 51097 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 74 total
• MANE Select transcript: NM_016002

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24275
Approved symbol	SCCPDH
Name	saccharopine dehydrogenase (putative)
Location	1q44
Locus type	gene with protein product
Status	Approved
Aliases	CGI-49, NET11
Ensembl gene	ENSG00000143653
Ensembl biotype	protein_coding
OMIM	620831
Entrez	51097

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 13 protein_coding

ENST00000366510, ENST00000878238, ENST00000878239, ENST00000878240, ENST00000878241, ENST00000878242, ENST00000878243, ENST00000878244, ENST00000878245, ENST00000878246, ENST00000878247, ENST00000878248, ENST00000878249

RefSeq mRNA: 1 — MANE Select: NM_016002 NM_016002

CCDS: CCDS31084

Canonical transcript exons

ENST00000366510 — 12 exons

Exon	Start	End
ENSE00000961412	246758226	246758356
ENSE00000961413	246759034	246759151
ENSE00000961414	246759957	246760076
ENSE00000961415	246760171	246760227
ENSE00000961416	246764246	246764357
ENSE00000961417	246766058	246766139
ENSE00001316184	246744076	246744125
ENSE00001616621	246767195	246768137
ENSE00002081704	246724409	246724612
ENSE00002397300	246735975	246736055
ENSE00002419383	246726892	246727004
ENSE00002426091	246740172	246740301

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 98.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 55.4726 / max 692.1113, expressed in 1815 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9556	49.1719	1815
9555	3.6003	1154
9553	1.0079	397
9552	0.7234	315
9554	0.4134	221
9557	0.2857	138
9558	0.2700	135

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.28	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.17	gold quality
right testis	UBERON:0004534	98.10	gold quality
spinal cord	UBERON:0002240	97.36	gold quality
testis	UBERON:0000473	97.26	gold quality
sperm	CL:0000019	96.96	gold quality
adrenal tissue	UBERON:0018303	96.92	gold quality
right lobe of liver	UBERON:0001114	96.36	gold quality
tibial nerve	UBERON:0001323	96.33	gold quality
adult organism	UBERON:0007023	96.32	gold quality
right adrenal gland	UBERON:0001233	96.22	gold quality
male germ cell	CL:0000015	96.20	gold quality
right adrenal gland cortex	UBERON:0035827	95.96	gold quality
left adrenal gland	UBERON:0001234	95.56	gold quality
left adrenal gland cortex	UBERON:0035825	95.19	gold quality
liver	UBERON:0002107	95.07	gold quality
adrenal gland	UBERON:0002369	94.80	gold quality
adrenal cortex	UBERON:0001235	94.74	gold quality
ventricular zone	UBERON:0003053	94.63	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.38	gold quality
medial globus pallidus	UBERON:0002477	94.31	gold quality
metanephros cortex	UBERON:0010533	94.19	gold quality
triceps brachii	UBERON:0001509	93.98	gold quality
pons	UBERON:0000988	93.79	gold quality
urinary bladder	UBERON:0001255	93.45	gold quality
gastrocnemius	UBERON:0001388	93.43	gold quality
substantia nigra	UBERON:0002038	93.22	gold quality
muscle of leg	UBERON:0001383	93.20	gold quality
islet of Langerhans	UBERON:0000006	92.87	gold quality
hypothalamus	UBERON:0001898	92.81	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	64.04
E-GEOD-134144	yes	31.17
E-HCAD-11	yes	27.18
E-MTAB-6701	yes	22.95
E-CURD-112	yes	18.84
E-CURD-46	yes	10.34
E-MTAB-6678	yes	8.51
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting SCCPDH, 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-1277-5P	100.00	73.95	5056
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	sccpdhb	ENSDARG00000024564
danio_rerio	sccpdha.2	ENSDARG00000075053
danio_rerio	sccpdha.1	ENSDARG00000075766
mus_musculus	Sccpdh	ENSMUSG00000038936
rattus_norvegicus	Sccpdh	ENSRNOG00000066712
drosophila_melanogaster	CG2604	FBGN0037298
drosophila_melanogaster	CG5167	FBGN0038038
caenorhabditis_elegans		WBGENE00017719
caenorhabditis_elegans		WBGENE00017720
caenorhabditis_elegans		WBGENE00021741

Protein

Protein identifiers

Saccharopine dehydrogenase-like oxidoreductase — Q8NBX0 (reviewed: Q8NBX0)

All UniProt accessions (2): Q8NBX0, A0A384NPM7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the saccharopine dehydrogenase family.

RefSeq proteins (1): NP_057086* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005097	Sacchrp_dh_NADP-bd	Domain
IPR036291	NAD(P)-bd_dom_sf	Homologous_superfamily
IPR051276	Saccharopine_DH-like_oxidrdct	Family

Pfam: PF03435

UniProt features (8 total): sequence conflict 3, modified residue 2, initiator methionine 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NBX0-F1	94.76	0.91

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 (2): 2, 217

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-114608	Platelet degranulation
R-HSA-109582	Hemostasis
R-HSA-76002	Platelet activation, signaling and aggregation
R-HSA-76005	Response to elevated platelet cytosolic Ca2+

MSigDB gene sets: 179 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, VERHAAK_AML_WITH_NPM1_MUTATED_DN, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_GLYCOLIPID_BIOSYNTHETIC_PROCESS, GOCC_SECRETORY_GRANULE, REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION, GOZGIT_ESR1_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, DOANE_RESPONSE_TO_ANDROGEN_DN, SMID_BREAST_CANCER_LUMINAL_B_UP, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS

GO Biological Process (1): glycolipid biosynthetic process (GO:0009247)

GO Molecular Function (1): oxidoreductase activity (GO:0016491)

GO Cellular Component (7): extracellular region (GO:0005576), nucleus (GO:0005634), mitochondrion (GO:0005739), lipid droplet (GO:0005811), membrane (GO:0016020), midbody (GO:0030496), platelet alpha granule lumen (GO:0031093)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Response to elevated platelet cytosolic Ca2+	1
Hemostasis	1
Platelet activation, signaling and aggregation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
intracellular membrane-bounded organelle	2
glycolipid metabolic process	1
lipid biosynthetic process	1
carbohydrate derivative biosynthetic process	1
catalytic activity	1
cytoplasm	1
intracellular membraneless organelle	1
platelet alpha granule	1
secretory granule lumen	1

Protein interactions and networks

STRING

996 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCCPDH	TCERG1L	Q5VWI1	524
SCCPDH	TMX3	Q96JJ7	467
SCCPDH	TMX4	Q9H1E5	462
SCCPDH	FOXRED1	Q96CU9	446
SCCPDH	TMEM53	Q6P2H8	446
SCCPDH	CDC14A	Q9UNH5	419
SCCPDH	TMEM209	Q96SK2	419
SCCPDH	NCLN	Q969V3	418
SCCPDH	TOR1AIP2	Q8NFQ8	418
SCCPDH	UTP15	Q8TED0	400
SCCPDH	SCAMP3	O14828	399
SCCPDH	SNX30	Q5VWJ9	399
SCCPDH	TMEM278	A6NKF7	396
SCCPDH	CHST8	Q9H2A9	391
SCCPDH	MRPS35	P82673	389

IntAct

117 interactions, top by confidence:

A	B	Type	Score
MED21	MED19	psi-mi:“MI:0914”(association)	0.880
DNAJB11	HSPA5	psi-mi:“MI:0914”(association)	0.830
DDB2	CCT2	psi-mi:“MI:0914”(association)	0.730
TAL2	TCF4	psi-mi:“MI:0914”(association)	0.670
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
BZW2	ENDOD1	psi-mi:“MI:0914”(association)	0.640
DDB2	CCT5	psi-mi:“MI:0914”(association)	0.640
TRDN	TMEM223	psi-mi:“MI:0914”(association)	0.640
C3AR1	TMEM120B	psi-mi:“MI:0914”(association)	0.530
BZW2	SLC27A2	psi-mi:“MI:0914”(association)	0.530
CPLX2	DEGS1	psi-mi:“MI:0914”(association)	0.530
SPRING1	PLSCR1	psi-mi:“MI:0914”(association)	0.530
PEX19	FAM20B	psi-mi:“MI:0914”(association)	0.530
rep	AGPS	psi-mi:“MI:0914”(association)	0.530
SLC39A4	TMEM120B	psi-mi:“MI:0914”(association)	0.530
RAB6B	SBF1	psi-mi:“MI:0914”(association)	0.530
SCCPDH	RPN1	psi-mi:“MI:0914”(association)	0.530
PEX19	MYO1D	psi-mi:“MI:0914”(association)	0.530
LIMK2	LIMK1	psi-mi:“MI:0914”(association)	0.530
SCCPDH	CCDC47	psi-mi:“MI:0915”(physical association)	0.400
	TK2	psi-mi:“MI:0915”(physical association)	0.400
PCNA	SCCPDH	psi-mi:“MI:0915”(physical association)	0.370
	ESYT2	psi-mi:“MI:0914”(association)	0.350
	E2F3	psi-mi:“MI:0914”(association)	0.350

BioGRID (256): SCCPDH (Affinity Capture-MS), SCCPDH (Affinity Capture-MS), SCCPDH (Affinity Capture-MS), SCCPDH (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), PDE4DIP (Affinity Capture-MS), RPN1 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), RAB4A (Affinity Capture-MS), USP13 (Affinity Capture-MS), SQSTM1 (Affinity Capture-MS), PAIP2 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), MIEN1 (Affinity Capture-MS), SAAL1 (Affinity Capture-MS)

ESM2 similar proteins: A1YER2, A1YFX9, A2T7G9, A6NNS2, B0BN93, B0BNF8, O22718, O35331, O35678, O75911, O77769, O80526, O88876, O95154, P11172, P14755, P15904, P84169, Q06136, Q15738, Q1RMJ5, Q28DS0, Q2KIJ5, Q2QNG7, Q2QZ86, Q3SZM9, Q3T067, Q3ZBE9, Q5E964, Q5I0K3, Q5PPL3, Q5R514, Q5R5C9, Q5RDZ2, Q6AY30, Q6UWP2, Q811X6, Q86WA6, Q8JGT5, Q8K183

Diamond homologs: A0PQ21, A1KMU7, A5U6W1, O53176, P9WGV4, P9WGV5, Q3T067, Q5R5C9, Q6AY30, Q7D745, Q7TXK2, Q8LGI2, Q8NBX0, Q8R127, Q9CD87, Q9GZE9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2141 predictions. Top by Δscore:

Variant	Effect	Δscore
1:246724608:GCTGG:G	donor_gain	1.0000
1:246724609:C:G	donor_gain	1.0000
1:246724611:GG:G	donor_gain	1.0000
1:246724612:GG:G	donor_gain	1.0000
1:246724747:G:GT	donor_gain	1.0000
1:246726885:A:AG	acceptor_gain	1.0000
1:246726888:TTA:T	acceptor_loss	1.0000
1:246726889:TAG:T	acceptor_loss	1.0000
1:246726890:A:AG	acceptor_gain	1.0000
1:246726890:A:C	acceptor_loss	1.0000
1:246726890:AG:A	acceptor_gain	1.0000
1:246726891:G:GA	acceptor_gain	1.0000
1:246726891:GG:G	acceptor_gain	1.0000
1:246726891:GGA:G	acceptor_gain	1.0000
1:246726891:GGAA:G	acceptor_gain	1.0000
1:246727000:GACCA:G	donor_gain	1.0000
1:246727001:ACCA:A	donor_gain	1.0000
1:246727002:CCA:C	donor_gain	1.0000
1:246727003:CA:C	donor_gain	1.0000
1:246727004:AGT:A	donor_loss	1.0000
1:246727005:GTA:G	donor_loss	1.0000
1:246727005:GTAA:G	donor_gain	1.0000
1:246727006:TAAG:T	donor_loss	1.0000
1:246727007:AA:A	donor_loss	1.0000
1:246727008:AGT:A	donor_loss	1.0000
1:246727009:G:GG	donor_gain	1.0000
1:246735973:A:AG	acceptor_gain	1.0000
1:246735974:G:GG	acceptor_gain	1.0000
1:246740271:G:GT	donor_gain	1.0000
1:246758224:AGG:A	acceptor_gain	1.0000

AlphaMissense

2788 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:246724481:G:A	G20D	0.998
1:246726995:C:G	C98W	0.998
1:246740253:T:C	S156P	0.998
1:246740271:G:A	G162R	0.998
1:246740271:G:C	G162R	0.998
1:246740272:G:A	G162E	0.998
1:246744096:A:C	S179R	0.998
1:246744098:T:A	S179R	0.998
1:246744098:T:G	S179R	0.998
1:246758250:T:A	W197R	0.998
1:246758250:T:C	W197R	0.998
1:246724463:G:A	G14D	0.997
1:246736010:T:G	C113W	0.997
1:246740172:T:C	F129L	0.997
1:246740174:T:A	F129L	0.997
1:246740174:T:G	F129L	0.997
1:246740251:A:T	D155V	0.997
1:246759092:G:C	D252H	0.997
1:246759114:C:T	T259I	0.997
1:246764261:T:C	F336L	0.997
1:246764263:C:A	F336L	0.997
1:246764263:C:G	F336L	0.997
1:246726994:G:A	C98Y	0.996
1:246736036:A:C	D122A	0.996
1:246736036:A:T	D122V	0.996
1:246736048:A:T	E126V	0.996
1:246740238:A:C	S151R	0.996
1:246740240:C:A	S151R	0.996
1:246740240:C:G	S151R	0.996
1:246740265:G:C	D160H	0.996

dbSNP variants (sampled 300 via entrez): RS1000015824 (1:246754231 G>A), RS1000034512 (1:246752432 A>G), RS1000101289 (1:246762023 T>G), RS1000166600 (1:246738336 C>A), RS1000199875 (1:246733867 G>A), RS1000240957 (1:246736807 T>A,C), RS1000283767 (1:246766554 A>C,G), RS1000288173 (1:246724978 G>A), RS1000335597 (1:246766886 C>G), RS1000436961 (1:246722918 T>A), RS1000514760 (1:246744680 A>G), RS1000522110 (1:246729171 A>G), RS1000588255 (1:246745045 A>T), RS1000588810 (1:246730315 C>T), RS1000623689 (1:246723213 G>A,C)

Disease associations

OMIM: gene MIM:620831 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST009391_341	Metabolite levels	6.000000e-06
GCST009391_418	Metabolite levels	2.000000e-06
GCST010243_139	Apolipoprotein B levels	6.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0010433	triacylglycerol 56:6 measurement
EFO:0010388	phosphatidylcholine 38:6 measurement
EFO:0004615	apolipoprotein B 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 cotreatment, decreases expression, affects expression	7
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	affects cotreatment, increases abundance, decreases expression	3
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Tretinoin	decreases expression	2
Aflatoxin B1	affects expression, decreases expression	2
Particulate Matter	decreases expression, increases abundance	2
dicrotophos	decreases expression	1
2,4,6-tribromophenol	decreases expression	1
tetrabromobisphenol A	decreases expression	1
manganese chloride	increases abundance, affects cotreatment, decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
tamibarotene	decreases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
acyline	increases expression	1
monomethylarsonous acid	increases expression	1
ICG 001	increases expression	1
bisphenol B	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
LDN 193189	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Arbutin	increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TK11	HAP1 SCCPDH (-) 1	Cancer cell line	Male
CVCL_XS48	HAP1 SCCPDH (-) 2	Cancer cell line	Male
CVCL_XS49	HAP1 SCCPDH (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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