TPD52L3

Chr 9

TPD52 like 3

Also known as: D55, NYDSP25, TPD55, hD55

This protein contains an N-terminal coiled-coil motif that enables formation of homo- and heteromeric complexes with other tumor protein D52-like family members and may function in spermatogenesis. Currently, no established human genetic diseases have been associated with mutations in this gene.

OMIMResearchSummary from RefSeq
MultiplemechanismLOEUF 1.54
Clinical SummaryTPD52L3
Population Constraint (gnomAD)
Low constraint (pLI 0.20) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
1.54LOEUF
pLI 0.198
Z-score 0.98
OE 0.36 (0.131.54)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-1.23Z-score
OE missense 1.40 (1.201.65)
103 obs / 73.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.36 (0.131.54)
00.351.4
Missense OE1.40 (1.201.65)
00.61.4
Synonymous OE0.97
01.21.6
LoF obs/exp: 1 / 2.7Missense obs/exp: 103 / 73.4Syn Z: 0.11
DN
0.86top 5%
GOF
0.75top 25%
LOF
0.1895th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

TPD52L3 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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