DEFB126

defensin beta 126, the group of Defensins, beta

Basic information

Region (hg38): 20:142589-145751

Previous symbols: [ "C20orf8" ]

Links

ENSG00000125788 ∙ NCBI:81623 ∙ OMIM:620131 ∙ HGNC:15900 ∙ Uniprot:Q9BYW3 ∙ 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 DEFB126 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB126 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			6	1		7
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	2

Variants in DEFB126

This is a list of pathogenic ClinVar variants found in the DEFB126 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-145447-G-A		not specified	Likely benign (Dec 18, 2023)
20-145468-T-C		not specified	Uncertain significance (Nov 18, 2022)
20-145513-G-A		not specified	Uncertain significance (Dec 15, 2023)
20-145514-GCAAA-G		not specified	Benign (Mar 29, 2016)
20-145549-C-T		not specified	Uncertain significance (Oct 17, 2023)
20-145564-G-C		not specified	Uncertain significance (Jul 09, 2021)
20-145640-C-T		not specified	Uncertain significance (Mar 24, 2023)
20-145658-C-T		not specified	Uncertain significance (Aug 14, 2023)
20-145669-ACC-A		not specified	Benign (Mar 29, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB126	protein_coding	protein_coding	ENST00000382398	2	3383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.408	0.478	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.262	68	62.2	1.09	0.00000321	711
Missense in Polyphen		9	6.9787	1.2896		70
Synonymous	-0.740	27	22.5	1.20	0.00000138	221
Loss of Function	0.986	0	1.13	0.00	4.80e-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: Highly glycosylated atypical beta-defensin involved in several aspects of sperm function. Facilitates sperm transport in the female reproductive tract and contributes to sperm protection against immunodetection; both functions are probably implicating the negative surface charge provided by its O-linked oligosaccharides in the sperm glycocalyx. Involved in binding of sperm to oviductal epithelial cells to form a sperm reservoir until ovulation. Release from the sperm surface during capacitation and ovaluation by an elevation of oviductal fluid pH is unmasking other surface components and allows sperm to penetrate the cumulus matrix and bind to the zona pellucida of the oocyte (By similarity). In vitro has antimicrobial activity and may inhibit LPS-mediated inflammation (PubMed:19373462, PubMed:23229569). {ECO:0000250|UniProtKB:Q9BEE3, ECO:0000269|PubMed:19373462, ECO:0000269|PubMed:23229569}.
• Disease: DISEASE: Note=May be involved in infertility. Homozygosity for frameshift truncating mutations are associated with reduced sperm O-linked glycan content, impaired sperm mobility and a reduced live birth rate (PubMed:21775668, PubMed:25721098). However, for one common mutation the change in sperm sialic acid levels has been challenged (PubMed:26832966). {ECO:0000269|PubMed:21775668, ECO:0000269|PubMed:25721098, ECO:0000305|PubMed:26832966}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System;Beta defensins;Defensins (Consensus)

Intolerance Scores

• loftool: 0.828
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.0127
• 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: 0.0718

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Defb22
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: single fertilization;innate immune response;defense response to Gram-negative bacterium;antimicrobial humoral immune response mediated by antimicrobial peptide
• Cellular component: extracellular region