LSP1

protein-coding

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

Gene summary

This gene encodes an intracellular F-actin binding protein. The protein is expressed in lymphocytes, neutrophils, macrophages, and endothelium and may regulate neutrophil motility, adhesion to fibrinogen matrix proteins, and transendothelial migration. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002339.3

Inheritance

—

ClinVar variants

U:7B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr11:1,850,904-1,892,267

External References & Databases

Ensembl (ENSG00000130592)

Transcript & Mutation Effects

hg38 • Region Span ~41.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LSP1 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 3

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002339.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	7	1	0	8

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002339.3	RefSeq	NP_002330.1	10	MANE Select
ENST00000311604.8	Ensembl	ENSP00000308383.4	10	MANE Select
NM_001013253.2	RefSeq	NP_001013271.1	9	Standard
NM_001013254.1	RefSeq	NP_001013272.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

C-type lectin receptor signaling pathway - Homo sapiens (human)
Tuberculosis - Homo sapiens (human)
p38 signaling mediated by MAPKAP kinases

Biological Process

cellular defense response
signal transduction

Molecular Function

actin binding

Cellular Component

plasma membrane
actin cytoskeleton
membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381775
Coding exons: 10
Length: 39298
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125744
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.528	237	261	0.908	0.0000146	3008
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.000097	rare
South Asian	0.000036	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in mediating neutrophil activation and chemotaxis. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.800
RVIS EVS: -0.04
RVIS percentile EVS: 50.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.417

Gene Damage Prediction

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