DEFB116

defensin beta 116, the group of Defensins, beta

Basic information

Region (hg38): 20:31303211-31308585

Links

ENSG00000215545 ∙ NCBI:245930 ∙ ∙ HGNC:18097 ∙ Uniprot:Q30KQ4 ∙ 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 DEFB116 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB116 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in DEFB116

This is a list of pathogenic ClinVar variants found in the DEFB116 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-31303217-T-C		not specified	Uncertain significance (Jun 11, 2021)
20-31303252-T-G		not specified	Uncertain significance (Jun 06, 2023)
20-31303265-C-T		not specified	Uncertain significance (Sep 09, 2021)
20-31303324-T-C		not specified	Uncertain significance (Feb 13, 2023)
20-31303328-G-C		not specified	Uncertain significance (Jan 26, 2022)
20-31303342-G-C		not specified	Uncertain significance (Mar 19, 2024)
20-31303387-C-G		not specified	Uncertain significance (Oct 06, 2023)
20-31303426-T-C		not specified	Uncertain significance (Jan 24, 2024)
20-31303434-G-T		not specified	Uncertain significance (Dec 21, 2023)
20-31303445-A-G		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB116	protein_coding	protein_coding	ENST00000400549	2	5374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00193	0.305	124739	0	4	124743	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.96	91	51.5	1.77	0.00000234	666
Missense in Polyphen		12	7.711	1.5562		111
Synonymous	-0.730	23	19.0	1.21	9.67e-7	178
Loss of Function	-1.46	3	1.24	2.41	5.24e-8	15

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has antibacterial activity. {ECO:0000250}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System;Beta defensins;Defensins (Consensus)

Intolerance Scores

• loftool: 0.611
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.00823
• 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: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Defb29

Gene ontology

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