LUZP2

leucine zipper protein 2

Basic information

Region (hg38): 11:24496969-25082638

Links

ENSG00000187398 ∙ NCBI:338645 ∙ OMIM:608178 ∙ HGNC:23206 ∙ Uniprot:Q86TE4 ∙ 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 LUZP2 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LUZP2 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						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	15	0	0

Variants in LUZP2

This is a list of pathogenic ClinVar variants found in the LUZP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-24729238-G-C		not specified	Uncertain significance (Dec 18, 2023)
11-24729261-T-C		not specified	Uncertain significance (May 11, 2022)
11-24738270-A-G		not specified	Uncertain significance (Sep 12, 2023)
11-24738294-C-G		not specified	Uncertain significance (May 23, 2023)
11-24738298-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-24905992-A-G		not specified	Uncertain significance (Mar 31, 2023)
11-24914532-A-T		not specified	Uncertain significance (Feb 17, 2023)
11-24914534-T-A		not specified	Uncertain significance (Feb 17, 2023)
11-24976597-C-A		not specified	Uncertain significance (Oct 20, 2021)
11-24983151-A-T		not specified	Uncertain significance (Nov 08, 2022)
11-24983166-G-T		not specified	Uncertain significance (Oct 12, 2022)
11-24983177-G-T		not specified	Uncertain significance (Apr 25, 2022)
11-24983184-G-A		not specified	Uncertain significance (May 25, 2022)
11-24983201-C-G		not specified	Uncertain significance (Feb 28, 2024)
11-24983267-C-G		not specified	Uncertain significance (Jan 04, 2022)
11-24983268-T-C		not specified	Uncertain significance (Feb 03, 2022)
11-24983290-C-G		not specified	Uncertain significance (Jul 14, 2022)
11-25077339-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-25077368-C-T		not specified	Uncertain significance (Apr 07, 2023)
11-25078569-C-T		not specified	Uncertain significance (Nov 14, 2023)
11-25078615-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LUZP2	protein_coding	protein_coding	ENST00000336930	12	585635

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.35e-10	0.257	125718	0	28	125746	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0296	166	167	0.994	0.00000833	2250
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000588	0.0000588
Ashkenazi Jewish	0.00	0.00
East Asian	0.000176	0.000163
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000188	0.000185
Middle Eastern	0.000176	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.781
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.8

Haploinsufficiency Scores

• pHI: 0.559
• hipred: N
• hipred_score: 0.267
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.229

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Luzp2
• Phenotype: normal phenotype

Gene ontology

• Cellular component: extracellular region