LIX1

limb and CNS expressed 1

Basic information

Region (hg38): 5:97091867-97142753

Previous symbols: [ "C5orf11" ]

Links

ENSG00000145721 ∙ NCBI:167410 ∙ OMIM:610466 ∙ HGNC:18581 ∙ Uniprot:Q8N485 ∙ 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 LIX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIX1 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in LIX1

This is a list of pathogenic ClinVar variants found in the LIX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-97094790-A-T		not specified	Uncertain significance (Sep 30, 2021)
5-97094989-C-T		not specified	Uncertain significance (Jun 18, 2021)
5-97096850-C-T		not specified	Uncertain significance (Feb 22, 2023)
5-97105248-A-T		not specified	Uncertain significance (Feb 17, 2024)
5-97107364-G-A		not specified	Uncertain significance (Dec 21, 2023)
5-97107395-T-C		not specified	Uncertain significance (May 06, 2022)
5-97107472-C-T		not specified	Uncertain significance (Aug 28, 2023)
5-97107473-G-A		not specified	Uncertain significance (Jan 02, 2024)
5-97124507-A-C		not specified	Uncertain significance (Dec 20, 2023)
5-97124624-C-T		not specified	Uncertain significance (Mar 15, 2024)
5-97142542-A-G		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIX1	protein_coding	protein_coding	ENST00000274382	6	51003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00196	0.979	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.281	145	155	0.936	0.00000811	1849
Missense in Polyphen		59	64.854	0.90973		735
Synonymous	0.401	54	57.9	0.933	0.00000293	540
Loss of Function	2.05	7	15.8	0.443	9.53e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000361	0.000359
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000317	0.000316
Middle Eastern	0.0000544	0.0000544
South Asian	0.000201	0.000196
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.763
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.365
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.538

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lix1
• Phenotype: normal phenotype

Gene ontology

• Biological process: autophagy;autophagosome maturation
• Cellular component: cytoplasm