LUZP4

leucine zipper protein 4, the group of Transcription and export complex 1 subunits

Basic information

Region (hg38): X:115289715-115307563

Links

ENSG00000102021 ∙ NCBI:51213 ∙ OMIM:300616 ∙ HGNC:24971 ∙ Uniprot:Q9P127 ∙ 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 LUZP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LUZP4 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				2	2	4
missense			14	5		19
nonsense			1			1
start loss						0
frameshift						0
inframe indel				3		3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	10	2

Variants in LUZP4

This is a list of pathogenic ClinVar variants found in the LUZP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-115289772-C-T			Likely benign (Mar 01, 2023)
X-115289845-C-T		not specified	Uncertain significance (May 18, 2023)
X-115302061-A-G		not specified	Uncertain significance (Jul 14, 2021)
X-115302093-T-C		not specified	Uncertain significance (Aug 31, 2022)
X-115302118-G-A		not specified	Likely benign (Mar 23, 2022)
X-115303365-T-G		not specified	Uncertain significance (Mar 31, 2024)
X-115303384-A-C		not specified	Uncertain significance (Jan 18, 2023)
X-115303394-A-C		not specified	Uncertain significance (Dec 09, 2023)
X-115306224-A-G		not specified	Uncertain significance (Oct 12, 2022)
X-115306256-T-A		not specified	Uncertain significance (Jun 29, 2023)
X-115306304-G-A		not specified	Uncertain significance (Apr 26, 2023)
X-115306318-A-G			Benign (Aug 08, 2017)
X-115306328-AATC-A			Likely benign (Apr 01, 2023)
X-115306349-C-T			Uncertain significance (Oct 01, 2019)
X-115306389-C-G		not specified	Uncertain significance (May 26, 2023)
X-115306399-G-A		LUZP4-related disorder	Likely benign (Mar 18, 2019)
X-115306400-C-G		not specified	Uncertain significance (May 16, 2023)
X-115306440-A-G		not specified	Uncertain significance (Jun 05, 2024)
X-115306462-A-G		LUZP4-related disorder	Benign (Jan 23, 2020)
X-115306480-CCACTCAGAGAGATCTCATGGT-C		LUZP4-related disorder	Likely benign (Apr 26, 2021)
X-115306497-A-T		not specified	Uncertain significance (Aug 14, 2023)
X-115306560-G-A		not specified	Likely benign (Mar 06, 2023)
X-115306611-GAGATCTCATAGCCACTCAGAA-G		LUZP4-related disorder	Likely benign (Nov 30, 2022)
X-115306612-A-T		not specified	Uncertain significance (Jul 13, 2022)
X-115306632-A-G			Likely benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LUZP4	protein_coding	protein_coding	ENST00000371920	4	17829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00139	0.442	100942	1	0	100943	0.00000495

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.669	133	113	1.18	0.00000829	2041
Missense in Polyphen		22	18.726	1.1748		364
Synonymous	0.353	37	39.8	0.929	0.00000297	576
Loss of Function	-0.107	4	3.77	1.06	2.37e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000743	0.0000484
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Export adapter involved in mRNA nuclear export in cancer cells. Binds and enhances the RNA-binding activity of the nuclear RNA export factor NXF1. Can restore mRNA export function in cells compromised by loss of mRNA export adapters (PubMed:25662211). {ECO:0000269|PubMed:25662211}.
• Pathway: Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0463

Intolerance Scores

• loftool: 0.802
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0163
• hipred: N
• hipred_score: 0.123
• ghis: 0.383

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0290

Gene Damage Prediction

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

Gene ontology

• Biological process: mRNA transport
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;protein binding