LUZP1

leucine zipper protein 1

Basic information

Region (hg38): 1:23084030-23178152

Links

ENSG00000169641 ∙ NCBI:7798 ∙ OMIM:601422 ∙ HGNC:14985 ∙ Uniprot:Q86V48 ∙ 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 LUZP1 gene.

• Inborn genetic diseases (36 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LUZP1 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			36	1	2	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	3

Variants in LUZP1

This is a list of pathogenic ClinVar variants found in the LUZP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-23088910-A-C		not specified	Uncertain significance (Jan 07, 2022)
1-23088992-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-23089001-G-C		not specified	Uncertain significance (Jan 05, 2022)
1-23091246-G-A		not specified	Uncertain significance (Aug 16, 2021)
1-23091248-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-23091336-G-C		not specified	Uncertain significance (Sep 13, 2023)
1-23091353-A-T		not specified	Uncertain significance (Nov 14, 2023)
1-23091432-C-T		not specified	Likely benign (Feb 17, 2022)
1-23091446-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-23091450-T-G		not specified	Uncertain significance (Mar 19, 2024)
1-23091481-C-G		not specified	Uncertain significance (Mar 07, 2024)
1-23091552-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-23091615-G-C		not specified	Uncertain significance (Nov 12, 2021)
1-23091635-C-T		not specified	Uncertain significance (Nov 09, 2021)
1-23091716-T-C		not specified	Uncertain significance (Nov 17, 2023)
1-23091740-G-A		not specified	Uncertain significance (Oct 27, 2023)
1-23091762-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-23091776-G-A		not specified	Uncertain significance (Apr 04, 2023)
1-23091788-T-A		not specified	Uncertain significance (Oct 10, 2023)
1-23091846-G-A		not specified	Uncertain significance (Jan 04, 2024)
1-23091900-C-G		not specified	Uncertain significance (Jan 19, 2022)
1-23091935-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-23092010-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-23092061-T-C		not specified	Uncertain significance (Dec 30, 2023)
1-23092083-T-C			Benign (Dec 14, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LUZP1	protein_coding	protein_coding	ENST00000302291	2	93786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.530	0.470	125721	0	26	125747	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.721	537	586	0.916	0.0000331	7060
Missense in Polyphen		137	178.96	0.76555		2332
Synonymous	-0.592	246	234	1.05	0.0000133	2165
Loss of Function	4.17	7	32.7	0.214	0.00000213	419

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000211	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000327	0.000163

dbNSFP

Source: dbNSFP

• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Intolerance Scores

• loftool: 0.429
• rvis_EVS: 0.34
• rvis_percentile_EVS: 73.73

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.384
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Luzp1
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; embryo phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: ventricular septum development;neural fold bending;artery development
• Cellular component: nucleus;membrane;extracellular exosome