DEFB129

Summary

DEFB129 (defensin beta 129, HGNC:16218) is a protein-coding gene on chromosome 20p13, encoding Beta-defensin 129 (Q9H1M3). Has antibacterial activity.

Defensins are cysteine-rich cationic polypeptides that are important in the immunologic response to invading microorganisms. The antimicrobial protein encoded by this gene is secreted and is a member of the beta defensin protein family. Beta defensin genes are found in several clusters throughout the genome, with this gene mapping to a cluster at 20p13.

Source: NCBI Gene 140881 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 26 total — 1 pathogenic
• MANE Select transcript: NM_080831

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16218
Approved symbol	DEFB129
Name	defensin beta 129
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	bA530N10.3, DEFB-29
Ensembl gene	ENSG00000125903
Ensembl biotype	protein_coding
Entrez	140881

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000246105

RefSeq mRNA: 1 — MANE Select: NM_080831 NM_080831

CCDS: CCDS12992

Canonical transcript exons

ENST00000246105 — 2 exons

Exon	Start	End
ENSE00001166546	229278	229886
ENSE00001491938	227258	227346

Expression profiles

Bgee: expression breadth broad, 13 present calls, max score 99.45.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8391 / max 1416.8262, expressed in 5 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182993	0.8314	5
182992	0.0078	1

Top tissues by expression

237 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	99.45	gold quality
cauda epididymis	UBERON:0004360	99.38	gold quality
sperm	CL:0000019	74.17	silver quality
seminal vesicle	UBERON:0000998	71.48	gold quality
caput epididymis	UBERON:0004358	59.11	silver quality
vena cava	UBERON:0004087	55.02	gold quality
sural nerve	UBERON:0015488	44.15	silver quality
upper leg skin	UBERON:0004262	43.71	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
inferior vagus X ganglion	UBERON:0005363	41.84	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
medulla oblongata	UBERON:0001896	40.40	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality
dorsal plus ventral thalamus	UBERON:0001897	40.10	gold quality
cartilage tissue	UBERON:0002418	40.06	gold quality
oviduct epithelium	UBERON:0004804	40.03	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting DEFB129, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-371A-5P	99.08	66.51	1914
HSA-MIR-3916	98.99	68.04	2155
HSA-MIR-6859-5P	98.99	68.07	2049
HSA-MIR-4277	98.34	67.17	1323
HSA-MIR-432-5P	98.00	68.13	989
HSA-MIR-6847-5P	97.93	66.74	1808
HSA-MIR-3198	97.84	65.64	579
HSA-MIR-3928-3P	97.61	66.53	1096
HSA-MIR-6892-5P	97.27	68.60	847
HSA-MIR-3907	96.76	65.04	662

Literature-anchored findings (GeneRIF, showing 1)

• The protein encoded by this gene is thought to display antimicrobial activity. (PMID:12620395)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Defb23	ENSMUSG00000074681
rattus_norvegicus	Defb23	ENSRNOG00000023477

Paralogs (19): DEFB127 (ENSG00000088782), DEFB118 (ENSG00000131068), DEFB104A (ENSG00000176782), DEFB104B (ENSG00000177023), DEFB125 (ENSG00000178591), DEFB124 (ENSG00000180383), DEFB123 (ENSG00000180424), DEFB119 (ENSG00000180483), DEFB108B (ENSG00000184276), DEFB128 (ENSG00000185982), DEFB131A (ENSG00000186146), DEFB132 (ENSG00000186458), DEFB121 (ENSG00000204548), DEFB134 (ENSG00000205882), DEFB135 (ENSG00000205883), DEFB108C (ENSG00000215371), DEFB116 (ENSG00000215545), DEFB115 (ENSG00000215547), DEFB131B (ENSG00000225805)

Protein

Protein identifiers

Beta-defensin 129 — Q9H1M3 (reviewed: Q9H1M3)

Alternative names: Beta-defensin 29, Defensin, beta 129

All UniProt accessions (2): Q9H1M3, A0A384MEC8

UniProt curated annotations — full annotation on UniProt →

Function. Has antibacterial activity.

Subcellular location. Secreted.

Tissue specificity. Expressed specifically in testis.

Similarity. Belongs to the beta-defensin family.

RefSeq proteins (1): NP_543021* (*=MANE)

Domains & families (InterPro)

UniProt features (8 total): disulfide bond 3, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H1M3-F1	60.57	0.14

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (3): 27–53, 34–48, 38–54

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1461957	Beta defensins
R-HSA-1461973	Defensins

MSigDB gene sets: 16 (showing top): REACTOME_INNATE_IMMUNE_SYSTEM, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, SRF_C, GOBP_DEFENSE_RESPONSE_TO_BACTERIUM, GOBP_RESPONSE_TO_BACTERIUM, REACTOME_ANTIMICROBIAL_PEPTIDES, MIR548P, MIR6892_5P, MIR3907, chr20p13, CCAWWNAAGG_SRF_Q4, GOBP_BIOLOGICAL_PROCESS_INVOLVED_IN_INTERSPECIES_INTERACTION_BETWEEN_ORGANISMS, REACTOME_DEFENSINS, REACTOME_BETA_DEFENSINS, MCCABE_BOUND_BY_HOXC6

GO Biological Process (2): defense response to bacterium (GO:0042742), defense response (GO:0006952)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Defensins	1
Antimicrobial peptides	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
defense response	1
response to bacterium	1
response to stress	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

322 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DEFB129	DEFB125	Q8N687	741
DEFB129	DEFB118	Q96PH6	726
DEFB129	DEFB127	Q9H1M4	690
DEFB129	DEFB128	Q7Z7B8	656
DEFB129	DEFB126	Q9BYW3	645
DEFB129	DEFB121	Q5J5C9	620
DEFB129	DEFB116	Q30KQ4	578
DEFB129	DEFB124	Q8NES8	541
DEFB129	DEFB110	Q30KQ9	540
DEFB129	DEFB113	Q30KQ7	531
DEFB129	DEFB112	Q30KQ8	521
DEFB129	DEFB132	Q7Z7B7	507
DEFB129	DEFB123	Q8N688	507
DEFB129	DEFB114	Q30KQ6	481
DEFB129	DEFB131A	P59861	478

IntAct

5 interactions, top by confidence:

A	B	Type	Score
TMED8	DEFB129	psi-mi:“MI:0915”(physical association)	0.560
DEFB129	NSG1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): DEFB129 (Two-hybrid), NSG1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVN3, A0A482APM8, A1KXM5, A4H257, A4H258, A4H259, A4H260, A6H7F9, A6NFE2, A6NHS7, A7KBS4, E9Q7F5, O74981, O75969, P09258, P09558, P19442, P22575, P80195, P88825, Q00997, Q04547, Q05100, Q2LCV6, Q2M2T8, Q30KK0, Q5NRP9, Q5QR91, Q5RAW4, Q5RBQ2, Q5RII3, Q6AXV6, Q6AXY9, Q6UW49, Q77NN4, Q7Z9I5, Q80YD3, Q810S2, Q8N4C9, Q95LJ2

Diamond homologs: A4H257, A4H258, A4H259, A4H260, Q30KK0, Q9H1M3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

26 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	21
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
816101	GRCh37/hg19 20p13(chr20:61568-1305971)x1	Pathogenic

SpliceAI

125 predictions. Top by Δscore:

Variant	Effect	Δscore
20:229276:A:AG	acceptor_gain	0.9700
20:229277:G:GG	acceptor_gain	0.9700
20:229277:GA:G	acceptor_gain	0.9600
20:229273:TACA:T	acceptor_loss	0.9400
20:229274:ACAG:A	acceptor_loss	0.9400
20:229275:CAG:C	acceptor_loss	0.9400
20:229276:AGAAT:A	acceptor_loss	0.9400
20:229277:G:C	acceptor_loss	0.9400
20:229580:A:G	acceptor_gain	0.9400
20:228980:C:G	donor_gain	0.9300
20:229277:GAAT:G	acceptor_gain	0.9300
20:229579:A:AG	acceptor_gain	0.9300
20:227345:AGGTA:A	donor_loss	0.9200
20:227346:GG:G	donor_loss	0.9200
20:229275:C:G	acceptor_gain	0.9100
20:229274:A:AG	acceptor_gain	0.8500
20:229277:GAA:G	acceptor_gain	0.8500
20:229277:GAATT:G	acceptor_gain	0.8300
20:229273:T:G	acceptor_gain	0.8100
20:228119:GC:G	donor_gain	0.8000
20:227349:A:C	donor_loss	0.7500
20:228348:TA:T	acceptor_gain	0.7500
20:228349:AA:A	acceptor_gain	0.7500
20:228350:AA:A	acceptor_gain	0.7500
20:229272:A:AG	acceptor_gain	0.7500
20:227340:A:AG	donor_gain	0.7400
20:227341:A:G	donor_gain	0.7400
20:227346:G:GC	donor_gain	0.7300
20:229579:AAAT:A	acceptor_gain	0.7300
20:227347:G:GC	donor_gain	0.7100

AlphaMissense

1212 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:229331:T:A	C38S	0.986
20:229332:G:C	C38S	0.986
20:227316:A:C	S10R	0.984
20:227318:C:A	S10R	0.984
20:227318:C:G	S10R	0.984
20:229298:T:C	C27R	0.983
20:229376:T:C	C53R	0.982
20:229361:T:A	C48S	0.981
20:229362:G:C	C48S	0.981
20:229361:T:C	C48R	0.980
20:229331:T:C	C38R	0.978
20:229319:T:A	C34S	0.977
20:229320:G:C	C34S	0.977
20:229376:T:A	C53S	0.976
20:229377:G:C	C53S	0.976
20:229298:T:A	C27S	0.974
20:229299:G:C	C27S	0.974
20:229319:T:C	C34R	0.974
20:229379:T:C	C54R	0.974
20:229379:T:A	C54S	0.971
20:229380:G:C	C54S	0.971
20:229332:G:A	C38Y	0.967
20:229300:T:G	C27W	0.966
20:229381:T:G	C54W	0.965
20:229333:C:G	C38W	0.963
20:229332:G:T	C38F	0.960
20:229380:G:A	C54Y	0.960
20:229378:T:G	C53W	0.958
20:229363:C:G	C48W	0.953
20:229321:C:G	C34W	0.952

dbSNP variants (sampled 300 via entrez): RS1000357475 (20:226723 T>C), RS1000831131 (20:226961 C>T), RS1001762648 (20:225259 C>A,G), RS1002253695 (20:227247 A>T), RS1002304388 (20:226892 A>G), RS1002589305 (20:228781 G>A), RS1002641512 (20:228443 G>A,C), RS1003219887 (20:228855 T>C,G), RS1004227000 (20:227416 G>A), RS1004257150 (20:226840 A>G), RS1004626084 (20:228084 C>A), RS1004671598 (20:226680 C>T), RS1004977239 (20:228405 A>G), RS1005235653 (20:225963 C>T), RS1006708654 (20:229598 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002658_3	Hirschsprung disease	4.000000e-06
GCST007010_4	Logical memory (delayed recall)	6.000000e-07
GCST007011_4	Logical memory (immediate recall)	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004874	memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	decreases expression	1
bisphenol A	increases expression	1
CGP 52608	increases reaction, affects binding	1
Vehicle Emissions	decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Nicotine	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.