LEXM

lymphocyte expansion molecule

Basic information

Region (hg38): 1:54806062-54842252

Previous symbols: [ "C1orf177" ]

Links

ENSG00000162398 ∙ NCBI:163747 ∙ OMIM:616446 ∙ HGNC:26854 ∙ Uniprot:Q3ZCV2 ∙ 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 LEXM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LEXM 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in LEXM

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

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

Position	Type	Phenotype	Significance	ClinVar
1-54806136-C-T		not specified	Uncertain significance (Nov 21, 2022)
1-54806152-C-G			Likely benign (Jun 01, 2022)
1-54806193-G-C		not specified	Uncertain significance (Feb 15, 2023)
1-54806207-G-A		not specified	Uncertain significance (Aug 23, 2021)
1-54806207-G-T		not specified	Uncertain significance (Mar 15, 2024)
1-54806214-G-A		not specified	Uncertain significance (Aug 28, 2023)
1-54807066-C-T		not specified	Uncertain significance (May 05, 2023)
1-54807067-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-54807078-C-G		not specified	Likely benign (Dec 27, 2023)
1-54807565-T-G		not specified	Uncertain significance (Mar 29, 2023)
1-54807629-C-T		not specified	Uncertain significance (Jun 02, 2024)
1-54807682-C-T		not specified	Uncertain significance (Apr 13, 2023)
1-54807911-C-A		not specified	Uncertain significance (Jan 27, 2022)
1-54807962-C-T		not specified	Uncertain significance (Aug 18, 2021)
1-54807964-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-54811831-G-A		not specified	Uncertain significance (Oct 26, 2021)
1-54811839-T-C		not specified	Uncertain significance (Mar 26, 2024)
1-54811870-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-54811885-G-C		not specified	Uncertain significance (Jun 17, 2024)
1-54811885-G-T		not specified	Uncertain significance (Sep 20, 2023)
1-54811901-G-A		not specified	Uncertain significance (May 06, 2024)
1-54811914-C-T		not specified	Uncertain significance (Apr 27, 2024)
1-54811920-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-54812118-A-C		not specified	Uncertain significance (Oct 05, 2023)
1-54812136-A-G		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LEXM	protein_coding	protein_coding	ENST00000371273	10	36190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.14e-13	0.0627	123466	25	2257	125748	0.00912

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.197	228	237	0.964	0.0000142	2701
Missense in Polyphen		90	79.449	1.1328		904
Synonymous	0.693	80	88.3	0.906	0.00000498	800
Loss of Function	0.486	21	23.5	0.892	0.00000141	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00767	0.00749
Ashkenazi Jewish	0.00341	0.00278
East Asian	0.000345	0.000326
Finnish	0.00941	0.00900
European (Non-Finnish)	0.0109	0.0101
Middle Eastern	0.000345	0.000326
South Asian	0.0290	0.0229
Other	0.0113	0.00916

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0859

Intolerance Scores

• rvis_EVS: 1.8
• rvis_percentile_EVS: 96.92

Haploinsufficiency Scores

• pHI: 0.0712
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lexm
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; neoplasm

Gene ontology

• Cellular component: mitochondrion