DEFB114

defensin beta 114, the group of Defensins, beta

Basic information

Region (hg38): 6:49960249-49964164

Links

ENSG00000177684 ∙ NCBI:245928 ∙ OMIM:615243 ∙ HGNC:18095 ∙ Uniprot:Q30KQ6 ∙ 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 DEFB114 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB114 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						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in DEFB114

This is a list of pathogenic ClinVar variants found in the DEFB114 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-49960386-T-C		not specified	Uncertain significance (Dec 08, 2023)
6-49960399-G-A		not specified	Uncertain significance (Jan 16, 2024)
6-49960404-T-C		not specified	Uncertain significance (Jan 16, 2024)
6-49960408-G-A		not specified	Uncertain significance (Feb 07, 2023)
6-49960419-C-T		not specified	Uncertain significance (Sep 13, 2023)
6-49960446-G-T		not specified	Uncertain significance (Oct 08, 2024)
6-49964063-A-T		not specified	Uncertain significance (Mar 01, 2024)
6-49964066-T-C		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB114	protein_coding	protein_coding	ENST00000322066	2	3857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0916	0.585	118426	0	1	118427	0.00000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.445	45	37.3	1.21	0.00000218	449
Missense in Polyphen		5	5.6632	0.88289		61
Synonymous	-0.371	12	10.5	1.15	4.51e-7	112
Loss of Function	0.00191	1	1.00	0.998	4.26e-8	12

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000361	0.0000361
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a salt-sensitive antimicrobial activity against Gram-negative bacteria, including E.coli, Gram-positive, including S.aureus, and fungi, including C.albicans. Binds to and neutralizes bacterial lipopolysaccharides (LPS), abolishing TNF production by macrophages challenged with LPS. Rescues the LPS- induced reduction of sperm motility in vitro and may protect from LPS-induced lethality. {ECO:0000269|PubMed:23482568}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System;Beta defensins;Defensins (Consensus)

Recessive Scores

• pRec: 0.0445

Intolerance Scores

• loftool: 0.422
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.0187
• hipred: N
• hipred_score: 0.146
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000668

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of lipopolysaccharide-mediated signaling pathway;negative regulation of MAP kinase activity;innate immune response;positive regulation of inflammatory response;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;antifungal innate immune response;negative regulation of tumor necrosis factor secretion
• Cellular component: extracellular region
• Molecular function: lipopolysaccharide binding