APCDD1L

Summary

APCDD1L (APC down-regulated 1 like, HGNC:26892) is a protein-coding gene on chromosome 20q13.32, encoding Protein APCDD1-like (Q8NCL9).

Predicted to enable Wnt-protein binding activity. Predicted to be involved in negative regulation of Wnt signaling pathway. Predicted to be located in plasma membrane.

Source: NCBI Gene 164284 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 104 total
• MANE Select transcript: NM_153360

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26892
Approved symbol	APCDD1L
Name	APC down-regulated 1 like
Location	20q13.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90166
Ensembl gene	ENSG00000198768
Ensembl biotype	protein_coding
Entrez	164284

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000371149, ENST00000425773, ENST00000491015, ENST00000853970

RefSeq mRNA: 2 — MANE Select: NM_153360 NM_001304787, NM_153360

CCDS: CCDS13467

Canonical transcript exons

ENST00000371149 — 4 exons

Exon	Start	End
ENSE00001288044	58470609	58470747
ENSE00001454465	58459101	58461554
ENSE00001454466	58514659	58515399
ENSE00002202171	58467106	58467658

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 89.56.

FANTOM5 (CAGE): breadth broad, TPM avg 4.5550 / max 151.7006, expressed in 712 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
188167	1.9060	484
188163	1.4810	530
188166	0.3642	203
188161	0.3045	153
188162	0.1976	94
188164	0.1570	90
188165	0.1213	73
188160	0.0233	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	89.56	silver quality
vena cava	UBERON:0004087	88.52	silver quality
stromal cell of endometrium	CL:0002255	87.24	gold quality
cartilage tissue	UBERON:0002418	85.64	gold quality
body of tongue	UBERON:0011876	84.00	silver quality
cardia of stomach	UBERON:0001162	83.96	silver quality
pericardium	UBERON:0002407	82.80	silver quality
tongue	UBERON:0001723	82.73	silver quality
cardiac muscle of right atrium	UBERON:0003379	81.96	gold quality
pharyngeal mucosa	UBERON:0000355	81.92	silver quality
left ventricle myocardium	UBERON:0006566	81.65	gold quality
trachea	UBERON:0003126	81.63	silver quality
superior surface of tongue	UBERON:0007371	81.62	gold quality
pylorus	UBERON:0001166	81.05	silver quality
renal medulla	UBERON:0000362	80.88	gold quality
lateral nuclear group of thalamus	UBERON:0002736	80.76	gold quality
nipple	UBERON:0002030	80.59	silver quality
pons	UBERON:0000988	80.52	silver quality
saphenous vein	UBERON:0007318	80.46	gold quality
substantia nigra pars compacta	UBERON:0001965	80.45	silver quality
substantia nigra pars reticulata	UBERON:0001966	79.89	gold quality
layer of synovial tissue	UBERON:0007616	79.47	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.02	silver quality
epithelium of mammary gland	UBERON:0003244	78.09	gold quality
mammary duct	UBERON:0001765	78.03	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.67	silver quality
superficial temporal artery	UBERON:0001614	76.91	gold quality
nasal cavity epithelium	UBERON:0005384	76.55	gold quality
islet of Langerhans	UBERON:0000006	76.33	gold quality
epithelial cell of pancreas	CL:0000083	76.31	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.06
E-MTAB-7249	no	18.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting APCDD1L, 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-9-5P	100.00	72.28	2361
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-3682-3P	99.58	67.63	865
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-4251	99.40	69.19	3363

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	apcdd1l	ENSDARG00000075557
rattus_norvegicus	Apcdd1l	ENSRNOG00000028440

Paralogs (1): APCDD1 (ENSG00000154856)

Protein

Protein identifiers

Protein APCDD1-like — Q8NCL9 (reviewed: Q8NCL9)

Alternative names: Adenomatosis polyposis coli down-regulated 1 protein-like

All UniProt accessions (2): Q8NCL9, A2A2P3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (2): NP_001291716, NP_699191* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029405	APCDD1_dom	Domain
IPR042425	APCDD1	Family

Pfam: PF14921

UniProt features (8 total): sequence variant 4, signal peptide 1, chain 1, transmembrane region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NCL9-F1	82.31	0.64

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): 150

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): NKX25_02, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, RIGGI_EWING_SARCOMA_PROGENITOR_DN, GOBP_NEGATIVE_REGULATION_OF_WNT_SIGNALING_PATHWAY, OSF2_Q6, GOMF_WNT_PROTEIN_BINDING, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, HATADA_METHYLATED_IN_LUNG_CANCER_UP, CHICAS_RB1_TARGETS_SENESCENT, JOHNSTONE_PARVB_TARGETS_1_DN, MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN, IRF5_TARGET_GENES, KMT2D_TARGET_GENES, ZNF512_TARGET_GENES, ZNF618_TARGET_GENES

GO Biological Process (1): negative regulation of Wnt signaling pathway (GO:0030178)

GO Molecular Function (2): Wnt-protein binding (GO:0017147), protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
negative regulation of signal transduction	1
Wnt signaling pathway	1
regulation of Wnt signaling pathway	1
protein binding	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

416 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
APCDD1L	ANKRD60	Q9BZ19	405
APCDD1L	OR10V1	Q8NGI7	380
APCDD1L	OR4F16	Q6IEY1	371
APCDD1L	OR8K5	Q8NH50	370
APCDD1L	OR10G8	Q8NGN5	359
APCDD1L	OR2T11	Q8NH01	356
APCDD1L	BEND2	Q8NDZ0	353
APCDD1L	MTMR6	Q9Y217	325
APCDD1L	ABLIM3	O94929	323
APCDD1L	TP53TG5	Q9Y2B4	321
APCDD1L	DCAF8	Q5TAQ9	312
APCDD1L	LPAR6	P43657	312
APCDD1L	CAMK2N2	Q96S95	311
APCDD1L	KRTAP1-5	Q9BYS1	306
APCDD1L	OR11H12	B2RN74	305

IntAct

10 interactions, top by confidence:

A	B	Type	Score
APCDD1L	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
APCDD1L	CYBC1	psi-mi:“MI:0915”(physical association)	0.560
APCDD1L	FXYD6	psi-mi:“MI:0915”(physical association)	0.560
YIPF1	APCDD1L	psi-mi:“MI:0915”(physical association)	0.000
CYBC1	APCDD1L	psi-mi:“MI:0915”(physical association)	0.000
FXYD6	APCDD1L	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): APCDD1L (Two-hybrid), APCDD1L (Two-hybrid), APCDD1L (Two-hybrid)

ESM2 similar proteins: A2A9Q0, A5PKD8, A9JSM3, D4A2Q0, E7ERA6, F1SAM7, F2Z333, P0CG25, Q07303, Q0IIA6, Q1RMK9, Q24JP5, Q2MJR0, Q2WF71, Q3MIP1, Q3UV16, Q3ZCQ3, Q504Y2, Q5EBM0, Q5GH56, Q5GH64, Q5GH72, Q5RJI4, Q5SZI1, Q641Q3, Q6IEE6, Q6IQX7, Q6P6N5, Q6UKI2, Q6ZMC9, Q6ZVW7, Q86UD0, Q8IUW3, Q8IZ52, Q8K064, Q8N4K4, Q8NAC3, Q8NBR0, Q8NCL9, Q8NFR9

Diamond homologs: Q3U128, Q5R2I8, Q5R2J4, Q66KI8, Q6DF34, Q8J025, Q8NCL9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	98
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1138 predictions. Top by Δscore:

Variant	Effect	Δscore
20:58467102:TCA:T	donor_loss	1.0000
20:58467104:A:AC	donor_gain	1.0000
20:58467104:ACCAG:A	donor_loss	1.0000
20:58467105:C:A	donor_loss	1.0000
20:58467105:C:CC	donor_gain	1.0000
20:58470607:AC:A	donor_gain	1.0000
20:58470608:CC:C	donor_gain	1.0000
20:58467105:CCA:C	donor_gain	0.9900
20:58467654:CGCAG:C	acceptor_gain	0.9900
20:58467655:GCAG:G	acceptor_gain	0.9900
20:58467656:CAG:C	acceptor_gain	0.9900
20:58467656:CAGC:C	acceptor_gain	0.9900
20:58467657:AG:A	acceptor_gain	0.9900
20:58467657:AGCT:A	acceptor_loss	0.9900
20:58467658:GC:G	acceptor_loss	0.9900
20:58467659:C:CA	acceptor_loss	0.9900
20:58467659:C:CC	acceptor_gain	0.9900
20:58467660:T:G	acceptor_loss	0.9900
20:58469932:G:C	donor_gain	0.9900
20:58461380:C:CT	acceptor_gain	0.9800
20:58461380:C:T	acceptor_gain	0.9800
20:58467104:AC:A	donor_gain	0.9800
20:58467105:CC:C	donor_gain	0.9800
20:58461555:C:CC	acceptor_gain	0.9700
20:58461559:C:CT	acceptor_gain	0.9700
20:58467099:CA:C	donor_gain	0.9700
20:58467105:CCAG:C	donor_gain	0.9700
20:58467662:C:CT	acceptor_gain	0.9700
20:58470602:GTCTT:G	donor_loss	0.9700
20:58470603:TCTTA:T	donor_loss	0.9700

AlphaMissense

3188 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:58461363:C:A	W311C	0.994
20:58461363:C:G	W311C	0.994
20:58467631:G:C	F72L	0.994
20:58467631:G:T	F72L	0.994
20:58467633:A:G	F72L	0.994
20:58470620:C:A	W59C	0.990
20:58470620:C:G	W59C	0.990
20:58461312:G:C	F328L	0.989
20:58461312:G:T	F328L	0.989
20:58461314:A:G	F328L	0.989
20:58467577:G:C	F90L	0.989
20:58467577:G:T	F90L	0.989
20:58467579:A:G	F90L	0.989
20:58467593:A:G	F85S	0.989
20:58467474:C:G	A125P	0.988
20:58461342:G:C	F318L	0.987
20:58461342:G:T	F318L	0.987
20:58461344:A:G	F318L	0.987
20:58461438:G:C	S286R	0.987
20:58461438:G:T	S286R	0.987
20:58461440:T:G	S286R	0.987
20:58467183:C:A	G222W	0.987
20:58467593:A:C	F85C	0.987
20:58470622:A:G	W59R	0.987
20:58470622:A:T	W59R	0.987
20:58461010:C:T	G429E	0.986
20:58461405:G:C	F297L	0.986
20:58461405:G:T	F297L	0.986
20:58461407:A:G	F297L	0.986
20:58467182:C:A	G222V	0.986

dbSNP variants (sampled 300 via entrez): RS1000007159 (20:58458807 G>A,T), RS1000226090 (20:58460235 G>A), RS1000246984 (20:58514955 G>T), RS1000341140 (20:58465139 G>T), RS1000400206 (20:58508982 G>T), RS1000402011 (20:58497269 C>T), RS1000410828 (20:58502888 T>C), RS1000436114 (20:58463668 G>T), RS1000459151 (20:58465577 C>T), RS1000528987 (20:58504045 G>A), RS1000550438 (20:58513408 G>A), RS1000562754 (20:58497848 A>C,T), RS1000582965 (20:58503722 G>A), RS1000607539 (20:58468016 G>A,C), RS1000612368 (20:58498212 A>G,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:182980, MIM:608627

GenCC curated gene-disease

Mondo (2): adult-onset proximal spinal muscular atrophy, autosomal dominant (MONDO:0008453), amyotrophic lateral sclerosis type 8 (MONDO:0012077)

Orphanet (2): Autosomal dominant adult-onset proximal spinal muscular atrophy (Orphanet:209335), Amyotrophic lateral sclerosis (Orphanet:803)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000789_2	Cardiovascular risk factors (age interaction)	1.000000e-06
GCST010173_98	Triglyceride levels	6.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0008007	age at assessment

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C563895	Amyotrophic Lateral Sclerosis 8 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	5
Benzo(a)pyrene	increases expression, affects methylation, decreases methylation	3
Aflatoxin B1	increases expression, increases methylation	3
Valproic Acid	affects cotreatment, increases expression, affects expression	2
Cadmium Chloride	increases expression	2
aristolochic acid I	increases expression	1
methyleugenol	increases expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
terbufos	increases methylation	1
benzo(e)pyrene	increases methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Acetaminophen	increases expression	1
Arsenic	affects methylation	1
Calcitriol	decreases expression	1
Copper	increases expression, affects binding	1
Dexamethasone	decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Disulfiram	affects binding, increases expression	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1
Estradiol	affects cotreatment, increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Hydrogen Peroxide	increases expression	1
Methapyrilene	increases methylation	1
Parathion	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	increases expression	1
Thiram	increases expression	1
Triclosan	decreases expression	1

Clinical trials (associated diseases)

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