DEFB129

defensin beta 129, the group of Defensins, beta

Basic information

Region (hg38): 20:227258-229886

Previous symbols: [ "C20orf87" ]

Links

ENSG00000125903 ∙ NCBI:140881 ∙ ∙ HGNC:16218 ∙ Uniprot:Q9H1M3 ∙ 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 DEFB129 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB129 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in DEFB129

This is a list of pathogenic ClinVar variants found in the DEFB129 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-227304-C-T		not specified	Uncertain significance (Feb 28, 2024)
20-227326-T-C		not specified	Uncertain significance (Sep 24, 2024)
20-229295-C-T		not specified	Uncertain significance (Dec 18, 2023)
20-229296-G-A		not specified	Uncertain significance (Aug 29, 2022)
20-229312-G-T		not specified	Likely benign (Aug 28, 2024)
20-229348-A-C		not specified	Uncertain significance (Feb 14, 2023)
20-229389-C-A		not specified	Uncertain significance (Jul 14, 2023)
20-229438-T-G		not specified	Uncertain significance (Mar 23, 2022)
20-229454-G-A		not specified	Uncertain significance (Nov 23, 2021)
20-229455-T-C		not specified	Uncertain significance (Dec 20, 2023)
20-229478-A-G		not specified	Uncertain significance (Sep 03, 2024)
20-229568-G-T		not specified	Uncertain significance (Jan 09, 2024)
20-229640-A-G		not specified	Uncertain significance (Jul 30, 2024)
20-229706-G-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
20-229707-C-T		not specified	Uncertain significance (Nov 08, 2021)
20-229714-T-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
20-229724-A-G		not specified	Uncertain significance (Nov 09, 2021)
20-229730-C-T		not specified	Uncertain significance (Jul 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB129	protein_coding	protein_coding	ENST00000246105	2	2629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0971	0.594	104282	0	32	104314	0.000153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.807	74	96.3	0.769	0.00000446	1205
Missense in Polyphen		9	16.601	0.54212		228
Synonymous	-0.675	39	34.0	1.15	0.00000165	353
Loss of Function	0.103	1	1.12	0.895	4.73e-8	13

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000814	0.0000814
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00130	0.00130
European (Non-Finnish)	0.0000401	0.0000401
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000206	0.000206

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: 0.0876

Intolerance Scores

• loftool: 0.665
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.284
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0547

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Defb23

Gene ontology

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