SCCPDH

saccharopine dehydrogenase (putative)

Basic information

Region (hg38): 1:246724408-246768137

Links

ENSG00000143653 ∙ NCBI:51097 ∙ ∙ HGNC:24275 ∙ Uniprot:Q8NBX0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCCPDH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCCPDH gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in SCCPDH

This is a list of pathogenic ClinVar variants found in the SCCPDH region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-246724507-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-246724544-C-T		not specified	Uncertain significance (Dec 12, 2023)
1-246726970-A-G		not specified	Uncertain significance (May 30, 2024)
1-246726996-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-246735979-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-246736004-A-T		not specified	Uncertain significance (Apr 08, 2023)
1-246740221-G-A		not specified	Uncertain significance (Jan 19, 2022)
1-246740254-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-246740283-A-G		not specified	Uncertain significance (May 17, 2023)
1-246758244-G-A		not specified	Uncertain significance (May 08, 2023)
1-246758264-T-G		not specified	Uncertain significance (Dec 19, 2022)
1-246758266-A-G		not specified	Uncertain significance (Dec 17, 2023)
1-246758287-A-C		not specified	Uncertain significance (Jun 04, 2024)
1-246758314-A-G		not specified	Uncertain significance (Mar 31, 2024)
1-246758331-C-T		not specified	Uncertain significance (Mar 02, 2023)
1-246758338-G-T		not specified	Uncertain significance (Dec 21, 2023)
1-246759052-T-G		not specified	Uncertain significance (Jun 11, 2024)
1-246760003-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-246760050-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-246760178-G-C		not specified	Uncertain significance (Nov 08, 2022)
1-246760210-G-A		not specified	Uncertain significance (May 11, 2022)
1-246760217-C-G		not specified	Uncertain significance (Oct 20, 2023)
1-246764303-G-C		not specified	Uncertain significance (Apr 08, 2024)
1-246764304-G-T		not specified	Uncertain significance (Apr 08, 2024)
1-246766090-G-A		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCCPDH	protein_coding	protein_coding	ENST00000366510	12	44091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.58e-9	0.597	125658	0	88	125746	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.977	183	224	0.816	0.0000108	2760
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000220	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000611	0.000607
Middle Eastern	0.000220	0.000217
South Asian	0.000310	0.000294
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.742
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.352
• hipred: N
• hipred_score: 0.443
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sccpdh

Gene ontology

• Biological process: platelet degranulation;glycolipid biosynthetic process;oxidation-reduction process
• Cellular component: extracellular region;nucleus;mitochondrion;lipid droplet;plasma membrane;membrane;midbody;platelet alpha granule lumen
• Molecular function: oxidoreductase activity