DEFB1

defensin beta 1, the group of Defensins, beta

Basic information

Region (hg38): 8:6870592-6877936

Links

ENSG00000164825

∙ NCBI:1672 ∙ OMIM:602056 ∙ HGNC:2766 ∙ Uniprot:P60022 ∙ 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 DEFB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB1 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					1 clinvar	1
missense			9 clinvar			9
nonsense				1 clinvar		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in DEFB1

This is a list of pathogenic ClinVar variants found in the DEFB1 region.

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

Position	Phenotype	Significance	ClinVar
8-6870697-G-C	not specified	Uncertain significance (Dec 14, 2023)	3081290
8-6870712-C-T	not specified	Uncertain significance (Jul 30, 2024)	3500786
8-6870718-C-G	not specified	Uncertain significance (Aug 21, 2023)	2620015
8-6870719-C-A	not specified	Uncertain significance (Feb 28, 2023)	2491110
8-6870734-A-C	not specified	Uncertain significance (Jun 03, 2024)	3271449
8-6870739-G-A	not specified	Uncertain significance (Oct 12, 2021)	2401997
8-6870739-G-T	not specified	Uncertain significance (Sep 17, 2021)	2349961
8-6870757-C-T	not specified	Uncertain significance (Feb 05, 2024)	3081289
8-6870777-G-T		Likely benign (May 30, 2018)	712566
8-6870790-T-C	not specified	Uncertain significance (Jun 26, 2024)	3500787
8-6870793-G-C	not specified	Uncertain significance (May 03, 2023)	2519814
8-6870798-G-C	not specified	Likely benign (Oct 29, 2024)	3500789
8-6870805-A-T	not specified	Uncertain significance (May 03, 2023)	2543082
8-6870807-G-A		Benign (May 31, 2018)	785241
8-6870817-A-C	not specified	Uncertain significance (Apr 12, 2022)	2214034
8-6877803-C-T	not specified	Uncertain significance (Aug 27, 2024)	3500788
8-6877813-C-G	not specified	Uncertain significance (Apr 17, 2024)	3271450

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB1	protein_coding	protein_coding	ENST00000297439	2	7448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.406	0.478	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.99	83	34.0	2.44	0.00000152	432
Missense in Polyphen		39	13.979	2.7899		144
Synonymous	-3.22	28	13.1	2.13	6.32e-7	128
Loss of Function	0.977	0	1.11	0.00	4.71e-8	13

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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Has bactericidal activity. May act as a ligand for C-C chemokine receptor CCR6. Positively regulates the sperm motility and bactericidal activity in a CCR6-dependent manner. Binds to CCR6 and triggers Ca2+ mobilization in the sperm which is important for its motility (PubMed:25122636). {ECO:0000269|PubMed:25122636}.;
Pathway: Antimicrobial peptides;Innate Immune System;Immune System;Beta defensins;Defensins (Consensus)

Recessive Scores

pRec: 0.255

Intolerance Scores

loftool: 0.660
rvis_EVS: -0.07
rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

pHI: 0.146
hipred: N
hipred_score: 0.146
ghis: 0.435

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.126

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Defb1
Phenotype: immune system phenotype; renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: innate immune response in mucosa;chemotaxis;immune response;G protein-coupled receptor signaling pathway;response to bacterium;antimicrobial humoral response;antibacterial humoral response;cAMP-mediated signaling;calcium-mediated signaling using intracellular calcium source;defense response to bacterium;innate immune response;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;positive regulation of flagellated sperm motility involved in capacitation;antimicrobial humoral immune response mediated by antimicrobial peptide
Cellular component: extracellular region;extracellular space;Golgi lumen;extrinsic component of membrane;extracellular exosome;sperm midpiece;microvesicle
Molecular function: protein binding;CCR6 chemokine receptor binding;identical protein binding