LZIC

leucine zipper and CTNNBIP1 domain containing

Basic information

Region (hg38): 1:9922113-9943407

Links

ENSG00000162441 ∙ NCBI:84328 ∙ OMIM:610458 ∙ HGNC:17497 ∙ Uniprot:Q8WZA0 ∙ 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 LZIC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LZIC 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in LZIC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-9930418-A-G		not specified	Uncertain significance (Feb 12, 2024)
1-9930419-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-9931920-C-A		not specified	Uncertain significance (Dec 17, 2023)
1-9931926-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-9932896-C-T		not specified	Uncertain significance (Mar 23, 2022)
1-9935526-A-G		not specified	Uncertain significance (Feb 28, 2024)
1-9935551-G-C		not specified	Uncertain significance (May 03, 2023)
1-9935619-A-C		not specified	Uncertain significance (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LZIC	protein_coding	protein_coding	ENST00000377223	6	21293

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00117	0.854	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.845	69	91.8	0.752	0.00000402	1245
Missense in Polyphen		15	24.945	0.60131		348
Synonymous	0.302	29	31.1	0.931	0.00000134	339
Loss of Function	1.26	6	10.4	0.578	4.34e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.754
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.198
• hipred: N
• hipred_score: 0.294
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lzic

Zebrafish Information Network

• Gene name: lzic
• Affected structure: neural tube
• Phenotype tag: abnormal
• Phenotype quality: degenerate

Gene ontology

• Biological process: response to ionizing radiation
• Molecular function: beta-catenin binding