TXLNG

protein-coding

taxilin gamma

Gene summary

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]

Previous symbols:

CXorf15

MANE transcript

NM_018360.3

Inheritance

—

ClinVar variants

U:135B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:16,786,432-16,844,519

External References & Databases

Ensembl (ENSG00000086712)

Transcript & Mutation Effects

hg38 • Region Span ~58.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TXLNG variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018360.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			14 clinvar	2 clinvar		16
missense			92 clinvar	3 clinvar	1 clinvar	96
nonsense			12 clinvar			12
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			17 clinvar			17
Total	0	0	135	5	1	141

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018360.3	RefSeq	NP_060830.2	10	MANE Select
ENST00000380122.10	Ensembl	ENSP00000369465.5	10	MANE Select
NM_001168683.2	RefSeq	NP_001162154.1	8	Standard
ENST00000398155.4	Ensembl	ENSP00000381222.4	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Validated transcriptional targets of AP1 family members Fra1 and Fra2

Biological Process

cell cycle
regulation of cell cycle process
regulation of bone mineralization
regulation of cell cycle

Molecular Function

syntaxin binding
protein heterodimerization activity

Cellular Component

cytosol
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380122
Coding exons: 10
Length: 58093
Individuals with no LoFs: 122733
Homozygous LoFs: 1
Heterozygous LoFs: 1
Defined: 122735
p: 0.00000815

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0863	181	184	0.982	0.0000141	3469
Missense (PolyPhen)		19	40.629	0.46764		946
Synonymous	-0.497	81	75.5	1.07	0.00000625	960
Loss of Function	4.02	0	18.8	0.00	0.00000149	327

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000025	0.0000089	rare
South Asian	0	0.0	absent
Other	0.00025	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in intracellular vesicle traffic. Inhibits ATF4-mediated transcription, possibly by dimerizing with ATF4 to form inactive dimers that cannot bind DNA. May be involved in regulating bone mass density through an ATF4-dependent pathway. May be involved in cell cycle progression. {ECO:0000269|PubMed:15911876, ECO:0000269|PubMed:18068885}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

RVIS EVS: 0.44
RVIS percentile EVS: 77.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium