SCCPDH

protein-coding

saccharopine dehydrogenase (putative)

Gene summary

Predicted to enable oxidoreductase activity. Predicted to be involved in glycolipid biosynthetic process. Located in lipid droplet and midbody. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016002.3

Inheritance

—

ClinVar variants

U:69

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr1:246,724,409-246,768,137

External References & Databases

Ensembl (ENSG00000143653)

Transcript & Mutation Effects

hg38 • Region Span ~43.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCCPDH variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 56

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016002.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			60 clinvar			60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	69	0	0	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016002.3	RefSeq	NP_057086.2	12	MANE Select
ENST00000366510.4	Ensembl	ENSP00000355467.3	12	MANE Select
ENST00000878238.1	Ensembl	ENSP00000548297.1	12	Standard
ENST00000878239.1	Ensembl	ENSP00000548298.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Platelet degranulation
Response to elevated platelet cytosolic Ca2+
Platelet activation, signaling and aggregation
Hemostasis

Biological Process

platelet degranulation
glycolipid biosynthetic process
oxidation-reduction process

Molecular Function

oxidoreductase activity

Cellular Component

extracellular region
nucleus
mitochondrion
lipid droplet
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366510
Coding exons: 12
Length: 44091
Individuals with no LoFs: 125658
Homozygous LoFs: 0
Heterozygous LoFs: 88
Defined: 125746
p: 0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.977	183	224	0.816	0.0000108	2760
Missense (PolyPhen)		43	55.091	0.78052		618
Synonymous	1.05	70	82.1	0.853	0.00000433	847
Loss of Function	1.21	16	22.1	0.723	0.00000103	289

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000090	0.000087	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00061	0.00061	rare
South Asian	0.00031	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.159

Intolerance Scores

LoFtool: 0.742
RVIS EVS: 0.26
RVIS percentile EVS: 70.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.175

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium