LNX1

ligand of numb-protein X 1, the group of PDZ domain containing|Ring finger proteins

Basic information

Region (hg38): 4:53459300-53701405

Previous symbols: [ "LNX" ]

Links

ENSG00000072201 ∙ NCBI:84708 ∙ OMIM:609732 ∙ HGNC:6657 ∙ Uniprot:Q8TBB1 ∙ 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 LNX1 gene.

• Inborn genetic diseases (25 variants)
• Lip and oral cavity carcinoma (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LNX1 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			24			24
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	25	0	0

Variants in LNX1

This is a list of pathogenic ClinVar variants found in the LNX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-53459394-C-T		not specified	Uncertain significance (Jul 25, 2023)
4-53459425-C-G		not specified	Uncertain significance (Jan 16, 2024)
4-53460936-T-A		not specified	Uncertain significance (Nov 10, 2022)
4-53460945-T-A		not specified	Uncertain significance (Dec 13, 2023)
4-53460993-T-G		not specified	Uncertain significance (Apr 25, 2023)
4-53461522-C-T		not specified	Uncertain significance (Aug 12, 2021)
4-53461570-A-G		not specified	Uncertain significance (Jan 23, 2024)
4-53476858-T-C		not specified	Uncertain significance (Mar 24, 2023)
4-53476880-C-T		not specified	Uncertain significance (Dec 09, 2023)
4-53476933-C-T		not specified	Uncertain significance (Feb 14, 2023)
4-53478643-T-C		not specified	Uncertain significance (Oct 13, 2023)
4-53478688-G-A		not specified	Uncertain significance (May 25, 2022)
4-53481769-C-T		not specified	Uncertain significance (Dec 09, 2023)
4-53481779-C-T		not specified	Likely benign (Jan 31, 2024)
4-53496042-C-T		not specified	Uncertain significance (Dec 20, 2023)
4-53496058-A-G		not specified	Uncertain significance (Jan 05, 2022)
4-53496165-T-C		not specified	Uncertain significance (Dec 04, 2023)
4-53496178-G-A		not specified	Uncertain significance (Oct 10, 2023)
4-53496187-T-C		not specified	Uncertain significance (Jul 08, 2022)
4-53496207-G-A		not specified	Uncertain significance (Dec 27, 2023)
4-53496246-C-T		not specified	Uncertain significance (May 04, 2023)
4-53496255-T-C		not specified	Uncertain significance (Oct 03, 2023)
4-53496256-A-C		not specified	Uncertain significance (May 26, 2022)
4-53496304-G-A		not specified	Uncertain significance (Oct 13, 2023)
4-53498778-C-G		not specified	Uncertain significance (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LNX1	protein_coding	protein_coding	ENST00000263925	10	242105

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000200	0.999	125636	0	112	125748	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0553	432	429	1.01	0.0000241	4761
Missense in Polyphen		143	161.7	0.88433		1893
Synonymous	0.623	159	169	0.939	0.00000998	1460
Loss of Function	2.86	15	32.6	0.460	0.00000198	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00170	0.00166
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000385	0.000381
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000384	0.000378
Middle Eastern	0.000385	0.000381
South Asian	0.000234	0.000229
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of NUMB. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Mediates ubiquitination of isoform p66 and isoform p72 of NUMB, but not that of isoform p71 or isoform p65. {ECO:0000250|UniProtKB:O70263}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Notch signaling pathway (Consensus)

Recessive Scores

• pRec: 0.158

Intolerance Scores

• loftool: 0.827
• rvis_EVS: -1.19
• rvis_percentile_EVS: 5.85

Haploinsufficiency Scores

• pHI: 0.314
• hipred: Y
• hipred_score: 0.756
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lnx1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;protein homooligomerization
• Cellular component: cytoplasm
• Molecular function: ubiquitin-protein transferase activity;protein binding;PDZ domain binding;metal ion binding