LSP1

lymphocyte specific protein 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 11:1850904-1892267

Links

ENSG00000130592 ∙ NCBI:4046 ∙ OMIM:153432 ∙ HGNC:6707 ∙ Uniprot:P33241 ∙ 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 LSP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSP1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	1	2	1

Variants in LSP1

This is a list of pathogenic ClinVar variants found in the LSP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-1853184-G-A		not specified	Uncertain significance (Nov 12, 2021)
11-1884518-C-A			Likely benign (Apr 01, 2022)
11-1889173-C-T			Benign (Feb 01, 2024)
11-1890570-A-G			Likely benign (Jun 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSP1	protein_coding	protein_coding	ENST00000381775	10	39298

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000147	0.961	125726	0	18	125744	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.528	237	261	0.908	0.0000146	3008
Missense in Polyphen		75	85.327	0.87897		1026
Synonymous	-0.827	124	113	1.10	0.00000734	924
Loss of Function	1.94	13	23.1	0.563	9.82e-7	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.0000967
Middle Eastern	0.000166	0.000163
South Asian	0.0000358	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in mediating neutrophil activation and chemotaxis. {ECO:0000250}.
• Pathway: C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);p38 signaling mediated by MAPKAP kinases (Consensus)

Intolerance Scores

• loftool: 0.800
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.386
• hipred: N
• hipred_score: 0.252
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.417

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lsp1
• Phenotype: hematopoietic system phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: cellular defense response;signal transduction
• Cellular component: plasma membrane;actin cytoskeleton;membrane;extracellular exosome
• Molecular function: actin binding