DEFB124

defensin beta 124, the group of Defensins, beta

Basic information

Region (hg38): 20:31465471-31476757

Links

ENSG00000180383 ∙ NCBI:245937 ∙ ∙ HGNC:18104 ∙ Uniprot:Q8NES8 ∙ 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 DEFB124 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB124 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6			6
Total	0	0	6	0	0

Variants in DEFB124

This is a list of pathogenic ClinVar variants found in the DEFB124 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-31476495-C-T		not specified	Uncertain significance (Jan 26, 2023)
20-31476504-C-T		not specified	Uncertain significance (Apr 12, 2022)
20-31476537-G-C		not specified	Uncertain significance (Nov 10, 2022)
20-31476555-C-T		not specified	Uncertain significance (May 14, 2024)
20-31476579-G-A		not specified	Uncertain significance (Oct 26, 2022)
20-31476579-G-C		not specified	Uncertain significance (Jun 30, 2024)
20-31476671-T-C		not specified	Uncertain significance (Apr 12, 2022)
20-31476690-G-A		not specified	Uncertain significance (Jan 29, 2024)
20-31476746-G-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB124	protein_coding	protein_coding	ENST00000317676	2	11252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.113	0.616	125471	0	1	125472	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.463	30	38.0	0.789	0.00000191	445
Missense in Polyphen		11	14.08	0.78125		173
Synonymous	0.561	15	18.0	0.832	0.00000105	143
Loss of Function	0.335	1	1.43	0.698	6.08e-8	16

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)	0.00000882	0.00000882
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.543
• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.89

Haploinsufficiency Scores

• pHI: 0.0102
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Defb25

Gene ontology

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