LPO

lactoperoxidase

Basic information

Region (hg38): 17:58218547-58268518

Links

ENSG00000167419 ∙ NCBI:4025 ∙ OMIM:150205 ∙ HGNC:6678 ∙ Uniprot:P22079 ∙ 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 LPO gene.

• Inborn genetic diseases (23 variants)
• not provided (7 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPO 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					3	3
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	0	23	0	8

Variants in LPO

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

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

Position	Type	Phenotype	Significance	ClinVar
17-58218600-A-G		Meckel-Gruber syndrome;Familial aplasia of the vermis	Likely benign (Oct 17, 2023)
17-58218605-C-A		Meckel-Gruber syndrome;Familial aplasia of the vermis	Likely benign (Oct 04, 2023)
17-58218608-C-T		Familial aplasia of the vermis;Meckel-Gruber syndrome	Likely benign (Jan 29, 2024)
17-58218609-G-A		Familial aplasia of the vermis;Meckel-Gruber syndrome	Likely benign (Jan 11, 2024)
17-58218609-G-C		Meckel-Gruber syndrome;Familial aplasia of the vermis	Likely benign (Oct 03, 2022)
17-58218610-T-TA		Familial aplasia of the vermis;Meckel-Gruber syndrome	Likely benign (May 09, 2023)
17-58218618-A-G		Bardet-Biedl syndrome 13;Meckel syndrome, type 1;Joubert syndrome 28 • Familial aplasia of the vermis;Meckel-Gruber syndrome • Meckel syndrome, type 1 • Joubert syndrome 28 • Bardet-Biedl syndrome 13	Likely pathogenic (Jan 08, 2024)
17-58218619-C-T		Familial aplasia of the vermis;Meckel-Gruber syndrome • Bardet-Biedl syndrome 13	Likely pathogenic (Mar 09, 2022)
17-58218619-CTGGCAGT-C		Meckel syndrome, type 1 • Bardet-Biedl syndrome 13;Joubert syndrome 28;Meckel syndrome, type 1 • Familial aplasia of the vermis;Meckel-Gruber syndrome • Bardet-Biedl syndrome 13 • MKS1-related disorder	Pathogenic/Likely pathogenic (Oct 16, 2023)
17-58218630-C-T		Meckel-Gruber syndrome;Familial aplasia of the vermis	Likely benign (Jan 04, 2024)
17-58218633-A-C		Familial aplasia of the vermis;Meckel-Gruber syndrome	Likely benign (Sep 09, 2020)
17-58218638-TA-T		Bardet-Biedl syndrome 13	Likely pathogenic (May 31, 2023)
17-58218645-G-T		Meckel-Gruber syndrome;Familial aplasia of the vermis	Likely benign (Mar 26, 2023)
17-58218647-C-T			Uncertain significance (Jan 30, 2018)
17-58218648-C-G		Familial aplasia of the vermis;Meckel-Gruber syndrome	Uncertain significance (Jun 12, 2022)
17-58218649-A-T		Familial aplasia of the vermis;Meckel-Gruber syndrome	Pathogenic (Apr 16, 2021)
17-58218651-G-A		Meckel-Gruber syndrome;Familial aplasia of the vermis	Likely benign (Jan 15, 2022)
17-58218660-GT-G		Meckel-Gruber syndrome;Familial aplasia of the vermis	Pathogenic (Jun 10, 2022)
17-58218662-C-T		Familial aplasia of the vermis;Meckel-Gruber syndrome	Uncertain significance (Aug 31, 2022)
17-58218663-C-T		Meckel-Gruber syndrome;Familial aplasia of the vermis	Likely benign (Feb 28, 2021)
17-58218666-C-G		Familial aplasia of the vermis;Meckel-Gruber syndrome	Likely benign (Aug 23, 2021)
17-58218669-G-A		Familial aplasia of the vermis;Meckel-Gruber syndrome	Likely benign (Oct 05, 2022)
17-58218669-G-T		Familial aplasia of the vermis;Meckel-Gruber syndrome	Likely benign (Feb 15, 2020)
17-58218674-C-A		Meckel-Gruber syndrome;Familial aplasia of the vermis	Pathogenic (Apr 24, 2021)
17-58218675-G-A		Meckel-Gruber syndrome;Familial aplasia of the vermis	Likely benign (Mar 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPO	protein_coding	protein_coding	ENST00000262290	12	49971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.50e-17	0.0571	125360	0	388	125748	0.00154

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	401	415	0.967	0.0000235	4629
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00206	0.00205
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000163	0.000163
Finnish	0.000739	0.000739
European (Non-Finnish)	0.00244	0.00244
Middle Eastern	0.000163	0.000163
South Asian	0.000784	0.000784
Other	0.00179	0.00179

dbNSFP

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}.
• Pathway: Salivary secretion - Homo sapiens (human);Purine metabolism (Consensus)

Recessive Scores

• pRec: 0.322

Intolerance Scores

• loftool: 0.804
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.46

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.296
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.909

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lpo
• Phenotype: vision/eye phenotype

Gene ontology

• 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;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: extracellular space;cytoplasm;basolateral plasma membrane;extracellular exosome
• Molecular function: peroxidase activity;heme binding;thiocyanate peroxidase activity;metal ion binding