LUZP1

protein-coding

leucine zipper protein 1

Gene summary

This gene encodes a protein that contains a leucine zipper motif. The exact function of the encoded protein is not known. In mice this gene affects neural tube closure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]

MANE transcript

NM_001395462.2

Inheritance

—

ClinVar variants

U:149B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr1:23,084,030-23,178,152

External References & Databases

Ensembl (ENSG00000169641)

Transcript & Mutation Effects

hg38 • Region Span ~94.1 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 LUZP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 149

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395462.2. 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			1 clinvar	5 clinvar	1 clinvar	7
missense			148 clinvar	7 clinvar	1 clinvar	156
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	149	12	2	163

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395462.2	RefSeq	NP_001382391.1	2	MANE Select
ENST00000302291.9	Ensembl	ENSP00000303758.4	2	MANE Select
NM_001142546.4	RefSeq	NP_001136018.1	2	Standard
NM_001395461.1	RefSeq	NP_001382390.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase

Biological Process

ventricular septum development
neural fold bending
artery development

Cellular Component

nucleus
membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302291
Coding exons: 2
Length: 93786
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 125747
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.721	537	586	0.916	0.0000331	7060
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00014	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00021	0.00015	rare
South Asian	0	0.0	absent
Other	0.00033	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.429
RVIS EVS: 0.34
RVIS percentile EVS: 73.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.970

Gene Damage Prediction

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