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…

LOFmechanismLOEUF 0.16

Clinical Summary— TXLNG

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

51 VUS of 151 total submissions

Explore recent and relevant literature in Research Assistant →

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?

0.16LOEUF

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

This gene — mechanism propensity

0.4586th %ile

GOF

0.4283th %ile

LOF

0.73top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.16

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

151 submitted variants in ClinVar

ClinVar

Classification Summary

VUS51

Likely Benign5

Benign1

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	51	0	51
Likely Benign	3	2	5
Benign	1	0	1
Total	55	2	57

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

73 pathogenic / likely-pathogenic (of 78) ClinVar copy-number / structural variants overlap TXLNG — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →