EDDM13

Summary

EDDM13 (epididymal protein 13, HGNC:53168) is a protein-coding gene on chromosome 19q13.43, encoding Epididymal protein 13 (A0A1B0GTR0).

Predicted to be located in extracellular region and membrane.

Source: NCBI Gene 100506374 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001354658

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53168
Approved symbol	EDDM13
Name	epididymal protein 13
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000267710
Ensembl biotype	protein_coding
Entrez	100506374

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding

ENST00000586573, ENST00000587247, ENST00000588154, ENST00000591188, ENST00000591810, ENST00000593116, ENST00000593151, ENST00000649256

RefSeq mRNA: 1 — MANE Select: NM_001354658 NM_001354658

CCDS: CCDS92694

Canonical transcript exons

ENST00000649256 — 15 exons

Exon	Start	End
ENSE00003831404	56276092	56276109
ENSE00003831945	56288385	56288438
ENSE00003831978	56295959	56295967
ENSE00003832853	56297505	56297531
ENSE00003834625	56288874	56288891
ENSE00003835215	56304793	56304830
ENSE00003835468	56301968	56302095
ENSE00003836668	56290841	56290846
ENSE00003836715	56284998	56285024
ENSE00003837923	56296336	56296362
ENSE00003837996	56282491	56282499
ENSE00003838543	56281693	56281698
ENSE00003838616	56310124	56310454
ENSE00003840131	56284198	56284206
ENSE00003843041	56272748	56272919

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 97.77.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5944 / max 282.3605, expressed in 196 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177710	0.2912	132
177705	0.0691	8
177711	0.0661	28
177707	0.0640	4
177709	0.0543	29
177706	0.0440	2
177708	0.0057	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	97.77	gold quality
skin of abdomen	UBERON:0001416	91.15	gold quality
cauda epididymis	UBERON:0004360	90.84	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.66	gold quality
skin of leg	UBERON:0001511	87.87	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.26	gold quality
zone of skin	UBERON:0000014	85.78	gold quality
sural nerve	UBERON:0015488	81.46	gold quality
lower esophagus mucosa	UBERON:0035834	79.31	gold quality
adrenal tissue	UBERON:0018303	77.91	gold quality
cerebellar cortex	UBERON:0002129	75.55	gold quality
cerebellar hemisphere	UBERON:0002245	75.45	gold quality
vagina	UBERON:0000996	75.40	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.38	gold quality
esophagus mucosa	UBERON:0002469	75.16	gold quality
upper leg skin	UBERON:0004262	74.95	gold quality
cardiac muscle of right atrium	UBERON:0003379	74.25	gold quality
left ventricle myocardium	UBERON:0006566	74.13	gold quality
colonic epithelium	UBERON:0000397	73.86	gold quality
cerebellum	UBERON:0002037	73.08	gold quality
right testis	UBERON:0004534	72.77	gold quality
calcaneal tendon	UBERON:0003701	72.21	gold quality
ectocervix	UBERON:0012249	71.74	gold quality
left testis	UBERON:0004533	71.73	gold quality
kidney epithelium	UBERON:0004819	71.50	gold quality
monocyte	CL:0000576	71.28	gold quality
leukocyte	CL:0000738	71.18	gold quality
upper arm skin	UBERON:0004263	70.98	gold quality
granulocyte	CL:0000094	70.49	gold quality
esophagus	UBERON:0001043	70.10	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.31

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Eddm13	ENSMUSG00000053367
rattus_norvegicus	Eddm13	ENSRNOG00000064702

Protein

Protein identifiers

Epididymal protein 13 — A0A1B0GTR0 (reviewed: A0A1B0GTR0)

All UniProt accessions (3): A0A1B0GTR0, A0A1B0GU87, A0A1B0GUE6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

RefSeq proteins (1): NP_001341587* (*=MANE)

Domains & families (InterPro)

UniProt features (3 total): signal peptide 1, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GTR0-F1	54.62	0.00

Functional residue map

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

Glycosylation sites (1): 56

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): PEREZ_TP63_TARGETS, PEREZ_TP53_AND_TP63_TARGETS, IRF5_TARGET_GENES, MAFG_TARGET_GENES, SOX3_TARGET_GENES, ZNF623_TARGET_GENES, ZSCAN5DP_TARGET_GENES, PEREZ_TP53_TARGETS, HE_LIM_SUN_FETAL_LUNG_C3_SCG3_POS_LYMPHATIC_ENDOTHELIAL_CELL, chr19q13

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): extracellular region (GO:0005576), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2

Protein interactions and networks

STRING

68 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EDDM13	C1orf232	A0A0U1RR37	829
EDDM13	CCDC201	A0A1B0GTI1	774
EDDM13	C10orf143	A0A1B0GUT2	769
EDDM13	SMIM36	A0A1B0GVT2	664
EDDM13	SMIM41	A0A2R8YCJ5	662
EDDM13	TMDD1	P0DPE3	644
EDDM13	SCYGR7	A0A286YF01	643
EDDM13	SMIM38	A0A286YFK9	643
EDDM13	FAM240C	A0A1B0GVR7	621
EDDM13	SMIM28	A0A1B0GU29	575
EDDM13	ETDA	Q3ZM63	529
EDDM13	ETDC	A0A1B0GVM5	528
EDDM13	SCYGR1	A0A286YEY9	480
EDDM13	SMIM31	A0A1B0GVY4	479
EDDM13	BTBD8	Q5XKL5	368

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0B4J1N3, A0A1B0GTK4, A0A1B0GTR0, A0JNL8, A2RUT3, A4IFR0, C9JUS6, D3ZKM3, E9PXB6, F2Z3F1, O70899, O71302, O93195, O95411, P03165, P04610, P0C7M3, P12912, P13206, P20976, P20977, P29560, P47939, P47940, P69714, Q02919, Q08648, Q1RN00, Q1WG82, Q5PR19, Q66669, Q67923, Q69027, Q69604, Q6PDA7, Q6UWK7, Q80IU5, Q80IU8, Q8N5N4, Q913A9

Diamond homologs: A0A1B0GTR0, E9Q7F5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

173 predictions. Top by Δscore:

Variant	Effect	Δscore
19:56281639:T:TA	donor_gain	0.9700
19:56281158:CT:C	donor_gain	0.9500
19:56283520:C:CT	donor_gain	0.9500
19:56283521:T:TT	donor_gain	0.9500
19:56281157:A:AC	donor_gain	0.9300
19:56281158:C:CC	donor_gain	0.9300
19:56300145:CCAGG:C	acceptor_gain	0.8900
19:56280631:T:C	donor_gain	0.8500
19:56287101:T:TA	donor_gain	0.8300
19:56297445:T:TA	donor_gain	0.8300
19:56299802:TTTG:T	donor_gain	0.8300
19:56283519:A:C	donor_gain	0.7500
19:56299804:TG:T	donor_gain	0.7500
19:56300146:CAGG:C	acceptor_gain	0.7500
19:56297450:T:A	donor_gain	0.7400
19:56299803:TTG:T	donor_gain	0.7400
19:56280234:T:TA	donor_gain	0.7100
19:56299805:G:T	donor_gain	0.6900
19:56306508:C:A	donor_gain	0.6800
19:56299801:TTTTG:T	donor_gain	0.6700
19:56302034:T:TA	acceptor_gain	0.6600
19:56280630:A:AC	donor_gain	0.6400
19:56297456:T:TA	donor_gain	0.6400
19:56281154:T:C	donor_gain	0.5900
19:56283581:T:A	donor_gain	0.5900
19:56300685:T:TA	donor_gain	0.5800
19:56306760:C:A	donor_gain	0.5800
19:56281602:A:C	donor_gain	0.5700
19:56281229:C:CT	acceptor_gain	0.5400
19:56281636:T:A	donor_gain	0.5000

AlphaMissense

1054 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:56302095:G:C	W141C	0.981
19:56302095:G:T	W141C	0.981
19:56310143:T:C	F161L	0.973
19:56310145:C:A	F161L	0.973
19:56310145:C:G	F161L	0.973
19:56302042:T:C	C124R	0.970
19:56296344:A:C	S84R	0.962
19:56296346:C:A	S84R	0.962
19:56296346:C:G	S84R	0.962
19:56310139:T:G	C159W	0.961
19:56310136:C:G	C158W	0.960
19:56302029:G:C	W119C	0.957
19:56302029:G:T	W119C	0.957
19:56304795:T:G	C142W	0.956
19:56302069:T:C	F133L	0.954
19:56302071:C:A	F133L	0.954
19:56302071:C:G	F133L	0.954
19:56310144:T:G	F161C	0.954
19:56304801:C:G	C144W	0.953
19:56304793:T:C	C142R	0.949
19:56302041:A:C	K123N	0.948
19:56302041:A:T	K123N	0.948
19:56302048:T:G	Y126D	0.947
19:56302093:T:A	W141R	0.947
19:56302093:T:C	W141R	0.947
19:56310137:T:C	C159R	0.947
19:56310137:T:A	C159S	0.945
19:56310138:G:C	C159S	0.945
19:56310134:T:C	C158R	0.944
19:56304810:T:G	C147W	0.940

dbSNP variants (sampled 300 via entrez): RS1000019743 (19:56302105 A>C), RS1000087570 (19:56298044 G>A), RS1000160610 (19:56296174 G>A), RS1000329835 (19:56310036 G>A), RS1000450683 (19:56290952 A>G), RS1000542955 (19:56298307 CA>C,CAA), RS1000605677 (19:56285463 C>G,T), RS1000625782 (19:56282523 T>C), RS1000630202 (19:56285298 G>T), RS1000680025 (19:56273640 C>A), RS1000847437 (19:56309798 G>A), RS1000892231 (19:56305713 C>G), RS1000918444 (19:56293802 T>G), RS1000951273 (19:56277085 C>T), RS1001032536 (19:56293583 C>T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
gallium arsenide	decreases expression	1
licochalcone B	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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