SEPSECS

Chr 4AR

Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase

Also known as: LP, PCH2D, SLA, SLA-p35, SLA/LP, SecS

NCBI Gene: 51091ENSG00000109618UniProt: Q9HD40OMIM: 613009

The amino acid selenocysteine is the only amino acid that does not have its own tRNA synthetase. Instead, this amino acid is synthesized on its cognate tRNA in a three step process. The protein encoded by this gene catalyzes the third step in the process, the conversion of O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec).[provided by RefSeq, Mar 2011]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Pontocerebellar hypoplasia type 2DMIM #613811
AR

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
11
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.99
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — SEPSECS
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.99LOEUF
pLI 0.000
Z-score 1.60
OE 0.65 (0.44–0.99)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.02Z-score
OE missense 1.00 (0.90–1.10)
269 obs / 270.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.65 (0.44–0.99)
0≤0.351.4
Missense OE?1.00 (0.90–1.10)
0≤0.61.4
Synonymous OE?0.73
0≤1.21.6
LoF obs/exp: 16 / 24.6Missense obs/exp: 269 / 270.0Syn Z: 2.10

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SEPSECS · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients