LTF

lactotransferrin, the group of Transferrins

Basic information

Region (hg38): 3:46435644-46485234

Links

ENSG00000012223 ∙ NCBI:4057 ∙ OMIM:150210 ∙ HGNC:6720 ∙ Uniprot:P02788 ∙ 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 LTF gene.

• Inborn genetic diseases (35 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTF 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				5	2	7
missense			31	5	3	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	10	5

Variants in LTF

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

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

Position	Type	Phenotype	Significance	ClinVar
3-46438081-A-G		not specified	Uncertain significance (Jan 20, 2023)
3-46438095-T-C		not specified	Likely benign (Jan 26, 2022)
3-46439324-C-T		not specified	Likely benign (Jul 09, 2021)
3-46439339-A-C		not specified	Uncertain significance (Dec 20, 2021)
3-46439363-G-A			Likely benign (Jan 01, 2023)
3-46439378-T-C		not specified	Uncertain significance (Feb 27, 2024)
3-46439418-C-T		not specified	Uncertain significance (Jan 02, 2024)
3-46441435-A-G			Likely benign (Oct 01, 2022)
3-46441477-C-G			Likely benign (Mar 29, 2018)
3-46443442-G-A		not specified	Uncertain significance (Oct 18, 2021)
3-46443494-A-C		not specified	Uncertain significance (Jul 11, 2023)
3-46443509-G-A			Likely benign (May 15, 2018)
3-46443532-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-46443552-C-A		not specified	Uncertain significance (Mar 14, 2023)
3-46445289-C-T		not specified	Uncertain significance (Jul 13, 2022)
3-46445302-G-C		not specified	Uncertain significance (Mar 04, 2024)
3-46445350-C-A			Benign (Jul 27, 2018)
3-46445421-G-A		not specified	Uncertain significance (Feb 03, 2022)
3-46446446-C-T			Benign (Jul 31, 2018)
3-46446449-G-T		not specified	Uncertain significance (Sep 16, 2021)
3-46447341-A-G		not specified	Uncertain significance (Jan 03, 2024)
3-46447398-T-C		not specified	Uncertain significance (Nov 09, 2021)
3-46448913-C-T		not specified	Uncertain significance (Sep 01, 2021)
3-46448915-C-A		not specified	Uncertain significance (Oct 22, 2021)
3-46448969-A-G		not specified	Uncertain significance (Oct 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTF	protein_coding	protein_coding	ENST00000231751	17	49589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-21	0.00883	125447	1	300	125748	0.00120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.226	432	419	1.03	0.0000248	4614
Missense in Polyphen		124	131.76	0.94112		1529
Synonymous	-0.556	183	174	1.05	0.0000114	1394
Loss of Function	0.714	35	39.9	0.878	0.00000226	440

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00885	0.00881
Ashkenazi Jewish	0.00	0.00
East Asian	0.000763	0.000761
Finnish	0.000337	0.000323
European (Non-Finnish)	0.000905	0.000897
Middle Eastern	0.000763	0.000761
South Asian	0.000296	0.000294
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.; FUNCTION: Lactoferricin binds to the bacterial surface and is crucial for the bactericidal functions. Has some antiviral activity against papillomavirus infection. N-terminal region shows strong antifungal activity against C.albicans. Contains two BBXB heparin-binding consensus sequences that appear to form the predominate functional GAG-binding site.; FUNCTION: Lactoferroxins A, B and C have opioid antagonist activity. Lactoferroxin A shows preference for mu-receptors, while lactoferroxin B and C have somewhat higher degrees of preference for kappa-receptors than for mu-receptors.; FUNCTION: Isoform DeltaLf: transcription factor with antiproliferative properties and ability to induce cell cycle arrest. Binds to the DeltaLf response element found in the SKP1, BAX, DCPS, and SELENOH promoters.
• Pathway: Neutrophil degranulation;Disease;Infectious disease;Antimicrobial peptides;Innate Immune System;Immune System;Mtb iron assimilation by chelation;Response of Mtb to phagocytosis;Latent infection of Homo sapiens with Mycobacterium tuberculosis;Metal sequestration by antimicrobial proteins (Consensus)

Recessive Scores

• pRec: 0.320

Intolerance Scores

• loftool: 0.943
• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.4

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.618

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ltf
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; neoplasm; normal phenotype; hematopoietic system phenotype; liver/biliary system phenotype; immune system phenotype

Gene ontology

• Biological process: ossification;regulation of cytokine production;retina homeostasis;innate immune response in mucosa;proteolysis;humoral immune response;antimicrobial humoral response;antibacterial humoral response;antifungal humoral response;killing of cells of other organism;negative regulation of lipopolysaccharide-mediated signaling pathway;regulation of tumor necrosis factor production;negative regulation of ATPase activity;siderophore-dependent iron import into cell;positive regulation of osteoblast proliferation;positive regulation of toll-like receptor 4 signaling pathway;negative regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;neutrophil degranulation;cellular protein metabolic process;negative regulation by host of viral process;negative regulation of viral genome replication;positive regulation of osteoblast differentiation;negative regulation of viral process;defense response to Gram-negative bacterium;positive regulation of NF-kappaB transcription factor activity;membrane disruption in other organism;bone morphogenesis;antimicrobial humoral immune response mediated by antimicrobial peptide;positive regulation of protein serine/threonine kinase activity;positive regulation of bone mineralization involved in bone maturation;negative regulation of single-species biofilm formation in or on host organism;positive regulation of chondrocyte proliferation;negative regulation of cysteine-type endopeptidase activity;negative regulation of tumor necrosis factor (ligand) superfamily member 11 production;negative regulation of osteoclast development
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;cell surface;secretory granule;protein-containing complex;specific granule lumen;specific granule;other organism cell membrane;extracellular exosome;phagocytic vesicle lumen;tertiary granule lumen
• Molecular function: lipopolysaccharide binding;DNA binding;serine-type endopeptidase activity;cysteine-type endopeptidase inhibitor activity;iron ion binding;protein binding;heparin binding;protein serine/threonine kinase activator activity