LPO

protein-coding

lactoperoxidase

Gene summary

This gene encodes a member of the peroxidase family of proteins. The encoded preproprotein is proteolytically processed to generate the mature enzyme. Following its secretion from salivary, mammary, and other mucosal glands, this enzyme catalyzes the generation of the antimicrobial substance hypothiocyanous acid. This gene is present in a gene cluster on chromosome 17. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

MANE transcript

NM_006151.3

Inheritance

—

ClinVar variants

U:108B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr17:58,218,548-58,268,518

External References & Databases

Ensembl (ENSG00000167419)

Transcript & Mutation Effects

hg38 • Region Span ~50.0 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 LPO variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006151.3. 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			1 clinvar	2 clinvar	3 clinvar	6
missense			107 clinvar	2 clinvar	1 clinvar	110
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	108	4	4	116

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006151.3	RefSeq	NP_006142.1	12	MANE Select
ENST00000262290.9	Ensembl	ENSP00000262290.4	12	MANE Select
NM_001160102.2	RefSeq	NP_001153574.1	10	Standard
ENST00000389576.4	Ensembl	ENSP00000374227.4	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Salivary secretion - Homo sapiens (human)
Purine metabolism

Biological Process

detection of chemical stimulus involved in sensory perception of bitter taste
response to oxidative stress
thiocyanate metabolic process
defense response to bacterium
hydrogen peroxide catabolic process

Molecular Function

peroxidase activity
heme binding
thiocyanate peroxidase activity
metal ion binding

Cellular Component

extracellular space
cytoplasm
basolateral plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262290
Coding exons: 12
Length: 49971
Individuals with no LoFs: 125360
Homozygous LoFs: 0
Heterozygous LoFs: 388
Defined: 125748
p: 0.00154

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.242	401	415	0.967	0.0000235	4629
Missense (PolyPhen)		196	193.29	1.014		2091
Synonymous	0.732	154	166	0.928	0.00000891	1446
Loss of Function	0.865	28	33.4	0.838	0.00000178	348

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00099	0.00098	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00074	0.00074	rare
European (Non-Finnish)	0.0024	0.0024	notable
South Asian	0.00078	0.00078	rare
Other	0.0018	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Antimicrobial agent which utilizes hydrogen peroxide and thiocyanate (SCN) to generate the antimicrobial substance hypothiocyanous acid (HOSCN) (By similarity). May contribute to airway host defense against infection. {ECO:0000250|UniProtKB:A5JUY8, ECO:0000269|PubMed:12626341}.;

Recessive Scores

pRec: 0.322

Intolerance Scores

LoFtool: 0.804
RVIS EVS: -1.24
RVIS percentile EVS: 5.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.909

Gene Damage Prediction

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