SPDEF

Chr 6

SAM pointed domain containing ETS transcription factor

Also known as: PDEF, bA375E1.3

NCBI Gene: 25803ENSG00000124664UniProt: O95238

The protein encoded by this gene belongs to the ETS family of transcription factors. It is highly expressed in the prostate epithelial cells, and functions as an androgen-independent transactivator of prostate-specific antigen (PSA) promoter. Higher expression of this protein has also been reported in brain, breast, lung and ovarian tumors, compared to the corresponding normal tissues, and it shows better tumor-association than other cancer-associated molecules, making it a more suitable target for developing specific cancer therapies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
1
Active trials
32
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.31
LOEUF· LoF intol.
LOF
Mechanism· predicted
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.31LOEUF
pLI 0.972
Z-score 3.40
OE 0.06 (0.02–0.31)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
0.80Z-score
OE missense 0.85 (0.75–0.96)
186 obs / 219.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.06 (0.02–0.31)
0≤0.351.4
Missense OE?0.85 (0.75–0.96)
0≤0.61.4
Synonymous OE?0.99
0≤1.21.6
LoF obs/exp: 1 / 15.4Missense obs/exp: 186 / 219.2Syn Z: 0.10

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SPDEF · 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