LUZP2

protein-coding

leucine zipper protein 2

Gene summary

This gene encodes a leucine zipper protein. This protein is deleted in some patients with Wilms tumor-Aniridia-Genitourinary anomalies-mental Retardation (WAGR) syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]

MANE transcript

NM_001009909.4

Inheritance

—

ClinVar variants

U:44B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr11:24,496,970-25,082,638

External References & Databases

Ensembl (ENSG00000187398)

Transcript & Mutation Effects

hg38 • Region Span ~585.7 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 LUZP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 44

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001009909.4. 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						0
missense			44 clinvar	1 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	1	0	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001009909.4	RefSeq	NP_001009909.2	12	MANE Select
ENST00000336930.11	Ensembl	ENSP00000336817.6	12	MANE Select
NM_001252008.2	RefSeq	NP_001238937.1	9	Standard
NM_001252010.2	RefSeq	NP_001238939.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336930
Coding exons: 12
Length: 585635
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125746
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0296	166	167	0.994	0.00000833	2250
Missense (PolyPhen)		68	63.606	1.0691		907
Synonymous	0.313	56	59.1	0.948	0.00000300	609
Loss of Function	0.784	17	20.9	0.815	0.00000103	279

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00018	0.00016	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.781
RVIS EVS: 0.44
RVIS percentile EVS: 77.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.229

Gene Damage Prediction

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