DEFB125

defensin beta 125, the group of Defensins, beta

Basic information

Region (hg38): 20:87250-97094

Links

ENSG00000178591 ∙ NCBI:245938 ∙ ∙ HGNC:18105 ∙ Uniprot:Q8N687 ∙ 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 DEFB125 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB125 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			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	0

Variants in DEFB125

This is a list of pathogenic ClinVar variants found in the DEFB125 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-87716-A-G		not specified	Uncertain significance (May 10, 2024)
20-87722-A-T		not specified	Uncertain significance (Jan 18, 2023)
20-87756-G-A		not specified	Likely benign (Aug 16, 2022)
20-96029-G-T		not specified	Uncertain significance (Oct 26, 2022)
20-96077-G-A		not specified	Uncertain significance (Mar 05, 2025)
20-96082-A-G		not specified	Uncertain significance (Jun 10, 2024)
20-96094-A-G		not specified	Uncertain significance (Nov 06, 2023)
20-96137-A-G		not specified	Uncertain significance (May 23, 2023)
20-96178-A-G		not specified	Uncertain significance (Dec 20, 2023)
20-96229-A-C		not specified	Uncertain significance (Feb 07, 2025)
20-96257-C-T		not specified	Uncertain significance (Apr 05, 2023)
20-96274-A-T		not specified	Uncertain significance (Sep 27, 2024)
20-96275-C-A		not specified	Uncertain significance (Sep 14, 2023)
20-96298-C-T		not specified	Uncertain significance (Aug 30, 2021)
20-96304-A-G		not specified	Uncertain significance (Nov 08, 2022)
20-96337-G-A		not specified	Likely benign (Mar 31, 2022)
20-96373-G-A		not specified	Likely benign (Sep 08, 2024)
20-96374-A-G		not specified	Uncertain significance (Feb 28, 2024)
20-96404-T-C		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB125	protein_coding	protein_coding	ENST00000382410	2	9845

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0145	0.463	125691	0	2	125693	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0452	87	85.8	1.01	0.00000402	1014
Missense in Polyphen		8	10.069	0.79454		126
Synonymous	0.184	29	30.3	0.957	0.00000139	322
Loss of Function	-0.788	2	1.11	1.81	4.70e-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)	0.00000903	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has antibacterial activity. {ECO:0000305}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System;Beta defensins;Defensins (Consensus)

Recessive Scores

• pRec: 0.0467

Intolerance Scores

• loftool: 0.646
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.11

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Defb26

Gene ontology

• Biological process: defense response to bacterium;innate immune response
• Cellular component: extracellular region