TEX12

Chr 11

testis expressed 12

NCBI Gene: 56158 ENSG00000150783 UniProt: Q9BXU0

The protein is a component of the transverse central element of synaptonemal complexes that form between homologous chromosomes during meiotic prophase and requires SYCP1 for incorporation into the central element. Mutations cause autosomal recessive male infertility due to meiotic arrest. The gene is not highly constrained in the general population, consistent with its specialized role in male reproductive function.

ResearchSummary from RefSeq, UniProt

This gene is similar to a mouse gene that is expressed in the testis. [provided by RefSeq, Jul 2008]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.78

LOEUF

Multiple*

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

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.78LOEUF

pLI 0.000

Z-score 0.09

OE 0.96 (0.49–1.78)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.30Z-score

OE missense 0.89 (0.71–1.12)

51 obs / 57.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.96 (0.49–1.78)

0≤0.351.4

Missense OE?0.89 (0.71–1.12)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 5 / 5.2Missense obs/exp: 51 / 57.3Syn Z: 0.06

Background carrier burden — how many people carry a rare variant somewhere in TEX12?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 920

129 rare PASS variants

Rare truncating (LoF)

1 in 18,000

15 rare PASS variants

Rare synonymous (reference)

1 in 950

60 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for TEX12. 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 1,100	1 in 27,000
South Asian	~43k	1 in 480	1 in 6,000
Remaining (unassigned)	~30k	1 in 750	none seen
European (Finnish)	~27k	1 in 1,800	none seen
Admixed American	~22k	1 in 400	none seen
African / African American	~21k	1 in 290	≈ 1 in 8,600
East Asian	~20k	1 in 890	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 930	none seen
Middle Eastern	~2,884	≈ 1 in 720	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): 3 of 4 coding exons well covered in gnomAD exomes; exon 5 marginal. Genomes: all 4.? see exons ↓