TPD52L3

Chr 9

TPD52 like 3

Also known as: D55, NYDSP25, TPD55, hD55

NCBI Gene: 89882 ENSG00000170777 UniProt: Q96J77 OMIM: 617567

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.

OMIM ResearchSummary from RefSeq

This gene encodes a member of the tumor protein D52-like family of proteins. These proteins are characterized by an N-terminal coiled-coil motif that is used to form homo- and heteromeric complexes with other tumor protein D52-like proteins. The encoded protein may play a role in spermatogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.54

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.54LOEUF

pLI 0.198

Z-score 0.98

OE 0.36 (0.13–1.54)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-1.23Z-score

OE missense 1.40 (1.20–1.65)

103 obs / 73.4 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.36 (0.13–1.54)

0≤0.351.4

Missense OE?1.40 (1.20–1.65)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 1 / 2.7Missense obs/exp: 103 / 73.4Syn Z: 0.11

Background carrier burden — how many people carry a rare variant somewhere in TPD52L3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 250

278 rare PASS variants

Rare truncating (LoF)

1 in 5,800

41 rare PASS variants

Rare synonymous (reference)

1 in 230

99 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for TPD52L3. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 460	1 in 8,700
South Asian	~43k	1 in 170	1 in 8,600
Remaining (unassigned)	~30k	1 in 180	1 in 3,000
European (Finnish)	~27k	1 in 2,400	none seen
Admixed American	~22k	1 in 140	≈ 1 in 5,600
African / African American	~21k	1 in 120	1 in 930
East Asian	~20k	1 in 270	1 in 1,200
Ashkenazi Jewish	~13k	1 in 1,500	≈ 1 in 2,600
Middle Eastern	~2,884	1 in 180	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓