LXN

latexin

Basic information

Region (hg38): 3:158645822-158672648

Links

ENSG00000079257 ∙ NCBI:56925 ∙ OMIM:609305 ∙ HGNC:13347 ∙ Uniprot:Q9BS40 ∙ 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 LXN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LXN 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					1	1
missense			3	4	2	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding				1	1	2
Total	0	0	4	5	4

Variants in LXN

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

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

Position	Type	Phenotype	Significance	ClinVar
3-158645968-A-G			Benign (Jul 09, 2018)
3-158646080-G-C			Likely benign (Jun 05, 2019)
3-158646151-G-A		not specified • Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Conflicting classifications of pathogenicity (Jan 31, 2024)
3-158646154-C-CT			Likely benign (Jan 09, 2024)
3-158646158-T-C			Likely benign (Oct 16, 2021)
3-158646164-G-A			Likely pathogenic (Jan 22, 2024)
3-158646168-A-G			Uncertain significance (Jun 25, 2013)
3-158646175-AAG-A		Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Pathogenic/Likely pathogenic (Oct 06, 2023)
3-158646178-A-T		Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1 • not specified	Conflicting classifications of pathogenicity (Jul 09, 2024)
3-158646179-T-C			Likely benign (Jun 09, 2023)
3-158646195-A-G			Uncertain significance (Jun 27, 2019)
3-158646198-G-C		Inborn genetic diseases	Uncertain significance (Feb 09, 2022)
3-158646201-TC-T		Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Pathogenic/Likely pathogenic (Aug 04, 2021)
3-158646209-A-G			Likely benign (Dec 26, 2023)
3-158646211-TAG-T		Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Likely pathogenic (Mar 20, 2024)
3-158646219-CAA-C		Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Pathogenic/Likely pathogenic (Mar 23, 2024)
3-158646221-A-G			Likely benign (Aug 02, 2023)
3-158646224-A-G			Likely benign (Oct 30, 2023)
3-158646225-G-T			Pathogenic (Feb 01, 2023)
3-158646232-C-CT		Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Pathogenic/Likely pathogenic (Jan 03, 2024)
3-158646233-T-C			Likely benign (Oct 31, 2023)
3-158646237-C-T			Pathogenic (Jun 06, 2023)
3-158646248-C-T			Likely benign (Dec 18, 2023)
3-158646249-A-G		Inborn genetic diseases	Uncertain significance (Nov 30, 2021)
3-158646252-T-TA		Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Likely pathogenic (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LXN	protein_coding	protein_coding	ENST00000264265	6	26872

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000183	0.451	125628	1	119	125748	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.748	89	111	0.800	0.00000498	1467
Missense in Polyphen		22	32.819	0.67034		422
Synonymous	0.187	40	41.5	0.963	0.00000221	393
Loss of Function	0.641	10	12.4	0.804	5.29e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000211
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000231	0.000229
Middle Eastern	0.000163	0.000163
South Asian	0.00286	0.00281
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hardly reversible, non-competitive, and potent inhibitor of CPA1, CPA2 and CPA4. May play a role in inflammation. {ECO:0000269|PubMed:15738388}.

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.813
• rvis_EVS: 1.26
• rvis_percentile_EVS: 93.53

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.131
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lxn
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: inflammatory response;negative regulation of endopeptidase activity;detection of temperature stimulus involved in sensory perception of pain
• Cellular component: cytoplasm
• Molecular function: protein binding;metalloendopeptidase inhibitor activity;heparin binding