TXLNA

taxilin alpha

Basic information

Region (hg38): 1:32179675-32198285

Links

ENSG00000084652 ∙ NCBI:200081 ∙ OMIM:608676 ∙ HGNC:30685 ∙ Uniprot:P40222 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TXLNA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXLNA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			30	1	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	2

Variants in TXLNA

This is a list of pathogenic ClinVar variants found in the TXLNA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-32180413-C-T		not specified	Uncertain significance (May 04, 2022)
1-32180424-C-T		not specified	Uncertain significance (Sep 22, 2023)
1-32180445-C-T		not specified	Uncertain significance (Dec 12, 2022)
1-32180465-A-G			Benign (Dec 31, 2019)
1-32180499-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-32181313-G-A		not specified	Uncertain significance (Jan 09, 2024)
1-32181364-G-C		not specified	Uncertain significance (Aug 16, 2021)
1-32181385-G-A		not specified	Uncertain significance (Mar 07, 2023)
1-32181461-A-G		not specified	Uncertain significance (Oct 14, 2021)
1-32181461-A-T		not specified	Uncertain significance (Aug 17, 2022)
1-32181548-C-T		not specified	Uncertain significance (Mar 28, 2022)
1-32181560-A-G		not specified	Uncertain significance (Jun 28, 2022)
1-32181572-G-A		not specified	Uncertain significance (Mar 29, 2022)
1-32184539-T-G		not specified	Uncertain significance (May 08, 2024)
1-32187990-C-T		not specified	Uncertain significance (May 03, 2023)
1-32188039-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-32188040-C-T		not specified	Likely benign (Mar 28, 2024)
1-32188050-A-C		not specified	Uncertain significance (Aug 20, 2023)
1-32188104-C-T		not specified	Uncertain significance (Dec 16, 2023)
1-32188111-A-G		not specified	Uncertain significance (Apr 16, 2024)
1-32190057-A-C		not specified	Uncertain significance (Sep 29, 2022)
1-32190159-C-G		not specified	Uncertain significance (Mar 14, 2023)
1-32190167-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-32190217-A-C		not specified	Uncertain significance (Jan 02, 2024)
1-32192316-C-G		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXLNA	protein_coding	protein_coding	ENST00000373609	10	18600

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00269	125732	0	4	125736	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	232	310	0.748	0.0000180	3559
Missense in Polyphen		46	102.8	0.44746		1207
Synonymous	0.884	112	125	0.899	0.00000686	1039
Loss of Function	4.38	2	26.2	0.0764	0.00000125	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000515	0.0000462
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000181	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in intracellular vesicle traffic and potentially in calcium-dependent exocytosis in neuroendocrine cells.
• Pathway: Other interleukin signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.0664
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.825
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.854

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txlna

Gene ontology

• Biological process: exocytosis;cell population proliferation;regulation of signaling receptor activity;cytokine-mediated signaling pathway;B cell activation
• Cellular component: extracellular region;cytoplasm;cytosol;membrane
• Molecular function: cytokine activity;protein binding;syntaxin binding;high molecular weight B cell growth factor receptor binding