TXLNG

Chr X

taxilin gamma

Also known as: CXorf15, ELRG, FIAT, LSR5, TXLNGX

NCBI Gene: 55787 ENSG00000086712 UniProt: Q9NUQ3

The protein binds to syntaxin family members and functions in intracellular vesicle trafficking, while also inhibiting ATF4-mediated transcription to regulate bone mass density and cell cycle progression. Mutations cause autosomal dominant neurodevelopmental disorders with intellectual disability and seizures. This gene is highly constrained against loss-of-function variants (pLI 0.998, LOEUF 0.158), indicating mutations are likely highly deleterious.

ResearchSummary from RefSeq, UniProt

This gene encodes a member of the taxilin family. The encoded protein binds to the C-terminal coiled-coil region of syntaxin family members 1A, 3A and 4A, and may play a role in intracellular vesicle trafficking. This gene is up-regulated by lipopolysaccharide and the gene product may be involved in cell cycle regulation. The related mouse protein was also shown to inhibit activating transcription factor 4-mediated transcription and thus regulate bone mass accrual. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

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.

Active trials

Pubs (1 yr)

—

P/LP submissions

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P/LP missense

0.16

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 — X-linked: males carry a single copy

LoF Constraint?

0.16LOEUF

pLI 0.998

Z-score 4.02

OE 0.00 (0.00–0.16)

Highly constrained

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

Missense Constraint?

0.09Z-score

OE missense 0.98 (0.87–1.11)

181 obs / 184.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.16)

0≤0.351.4

Missense OE?0.98 (0.87–1.11)

0≤0.61.4

Synonymous OE?1.07

0≤1.21.6

LoF obs/exp: 0 / 18.8Missense obs/exp: 181 / 184.3Syn Z: -0.50

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

gnomAD v4 · ~732k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

423 rare PASS variants

Rare truncating (LoF)

1 in 2,200

27 rare PASS variants

Rare synonymous (reference)

1 in 190

193 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for TXLNG. 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)	~561k	1 in 170	1 in 2,500
South Asian	~36k	1 in 160	1 in 2,300
Remaining (unassigned)	~31k	1 in 130	1 in 2,300
European (Finnish)	~27k	1 in 680	1 in 1,500
Admixed American	~23k	1 in 180	1 in 630
African / African American	~21k	1 in 210	1 in 1,200
East Asian	~20k	1 in 130	1 in 1,500
Ashkenazi Jewish	~13k	1 in 570	1 in 1,800
Middle Eastern	~2,758	1 in 330	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): 9 of 10 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 10.? see exons ↓