DEFB104A

defensin beta 104A, the group of Defensins, beta

Basic information

Region (hg38): 8:7836436-7841242

Previous symbols: [ "DEFB104" ]

Links

ENSG00000176782 ∙ NCBI:140596 ∙ ∙ HGNC:18115 ∙ Uniprot:Q8WTQ1 ∙ 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 DEFB104A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB104A 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						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in DEFB104A

This is a list of pathogenic ClinVar variants found in the DEFB104A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-7836512-A-G			Benign (Jun 26, 2017)
8-7836534-A-G		not specified	Uncertain significance (Jul 13, 2021)
8-7841042-G-C		not specified	Uncertain significance (Aug 09, 2021)
8-7841053-G-C		not specified	Uncertain significance (Jan 08, 2024)
8-7841087-C-T		not specified	Uncertain significance (Mar 07, 2023)
8-7841099-C-T		not specified	Uncertain significance (Aug 02, 2021)
8-7841112-A-G		not specified	Uncertain significance (Jul 26, 2022)
8-7841190-C-A		not specified	Likely benign (Nov 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB104A	protein_coding	protein_coding	ENST00000314265	2	4772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0937	0.589	107039	0	1	107040	0.00000467

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.202	28	31.2	0.898	0.00000158	422
Missense in Polyphen		8	9.1744	0.872		82
Synonymous	0.735	8	11.1	0.719	5.61e-7	123
Loss of Function	0.0438	1	1.05	0.954	4.46e-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)	0.0000101	0.0000101
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has antimicrobial activity. Synergistic effects with lysozyme and DEFB103. {ECO:0000269|PubMed:11481241}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System;Beta defensins;Defensins (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.739
• rvis_EVS: 0.61
• rvis_percentile_EVS: 83

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.238
• ghis: 0.414

Essentials

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

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

• Biological process: monocyte chemotaxis;innate immune response;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;positive chemotaxis;cellular response to phorbol 13-acetate 12-myristate
• Cellular component: extracellular region
• Molecular function: chemoattractant activity