SCCPDH

Chr 1

saccharopine dehydrogenase (putative)

Also known as: CGI-49, CGI49, NET11

NCBI Gene: 51097 ENSG00000143653 UniProt: Q8NBX0

The protein is predicted to function as an oxidoreductase involved in glycolipid biosynthesis and is localized to lipid droplets and the midbody. This gene shows no strong constraint against loss-of-function variants (pLI near zero, LOEUF >1), and no established disease associations have been reported in the provided data.

ResearchSummary from RefSeq

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]

ResearchGenerating clinical summary…

LOEUF 1.10

Clinical Summary— SCCPDH

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

56 VUS of 77 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.10LOEUF

pLI 0.000

Z-score 1.21

OE 0.72 (0.49–1.10)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.98Z-score

OE missense 0.82 (0.72–0.92)

183 obs / 224.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.72 (0.49–1.10)

0≤0.351.4

Missense OE?0.82 (0.72–0.92)

0≤0.61.4

Synonymous OE?0.85

0≤1.21.6

LoF obs/exp: 16 / 22.1Missense obs/exp: 183 / 224.2Syn Z: 1.05

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

VUS56

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	56	56
Likely Benign	0	0
Benign	0	0
Total	56	56

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

75 pathogenic / likely-pathogenic (of 98) ClinVar copy-number / structural variants overlap SCCPDH — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →