CCDC163

Summary

CCDC163 (CCDC163 homolog, HGNC:27003) is a protein-coding gene on chromosome 1p34.1, encoding Transmembrane protein CCDC163 (A0A0D9SF12).

Predicted to be located in membrane.

Source: NCBI Gene 126661 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001102601

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27003
Approved symbol	CCDC163
Name	CCDC163 homolog
Location	1p34.1
Locus type	gene with protein product
Status	Approved
Aliases	LOC126661
Ensembl gene	ENSG00000280670
Ensembl biotype	protein_coding
Entrez	126661

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 7 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000625766, ENST00000626177, ENST00000626657, ENST00000628293, ENST00000628397, ENST00000629009, ENST00000629482, ENST00000629670, ENST00000877907, ENST00000924179, ENST00000924180, ENST00000924181, ENST00000971908

RefSeq mRNA: 3 — MANE Select: NM_001102601 NM_001102601, NM_001358406, NM_001358407

CCDS: CCDS85969

Canonical transcript exons

ENST00000629482 — 5 exons

Exon	Start	End
ENSE00003761067	45497299	45497383
ENSE00003767558	45496556	45496623
ENSE00003768802	45493866	45495166
ENSE00003774294	45499345	45499443
ENSE00003842027	45499532	45500073

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 86.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.8740 / max 47.4731, expressed in 1218 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12124	1.8236	846
12122	0.7087	458
12123	0.3416	171

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	86.65	gold quality
secondary oocyte	CL:0000655	85.95	gold quality
buccal mucosa cell	CL:0002336	82.29	gold quality
granulocyte	CL:0000094	81.95	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	81.36	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.21	gold quality
spinal cord	UBERON:0002240	79.32	gold quality
hypothalamus	UBERON:0001898	78.43	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.02	silver quality
body of pancreas	UBERON:0001150	78.00	gold quality
substantia nigra	UBERON:0002038	76.70	gold quality
oviduct epithelium	UBERON:0004804	76.28	gold quality
medial globus pallidus	UBERON:0002477	76.21	gold quality
ventricular zone	UBERON:0003053	75.26	gold quality
pancreas	UBERON:0001264	74.49	gold quality
right atrium auricular region	UBERON:0006631	74.10	gold quality
amygdala	UBERON:0001876	74.01	gold quality
midbrain	UBERON:0001891	73.96	gold quality
cardiac atrium	UBERON:0002081	73.32	gold quality
anterior cingulate cortex	UBERON:0009835	73.17	gold quality
right frontal lobe	UBERON:0002810	72.98	gold quality
right ovary	UBERON:0002118	72.88	gold quality
globus pallidus	UBERON:0001875	72.80	gold quality
adenohypophysis	UBERON:0002196	72.20	gold quality
caudate nucleus	UBERON:0001873	72.16	gold quality
islet of Langerhans	UBERON:0000006	72.08	gold quality
smooth muscle tissue	UBERON:0001135	72.07	gold quality
right adrenal gland cortex	UBERON:0035827	71.50	gold quality
Brodmann (1909) area 9	UBERON:0013540	71.38	gold quality
mucosa of transverse colon	UBERON:0004991	70.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.27

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Transmembrane protein CCDC163 — A0A0D9SF12 (reviewed: A0A0D9SF12)

Alternative names: Coiled-coil domain-containing protein 163, coiled-coil domain containing 163 pseudogene

All UniProt accessions (5): A0A0D9SF12, A0A0D9SEU7, A0A0D9SFD8, A0A0D9SG11, B4DV03

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (3): NP_001096071, NP_001345335, NP_001345336 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039284	CCDC159/163	Family

UniProt features (2 total): chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A0D9SF12-F1	59.57	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): chr1p34, MARSON_BOUND_BY_E2F4_UNSTIMULATED, SANSOM_APC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, ASH1L_TARGET_GENES, ATF6_TARGET_GENES, BARX1_TARGET_GENES, CBX7_TARGET_GENES, DIDO1_TARGET_GENES, DLX4_TARGET_GENES, E2F5_TARGET_GENES, FOXD2_TARGET_GENES, HHEX_TARGET_GENES, HOXB4_TARGET_GENES, HOXC6_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

98 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC163	ZNF266	Q14584	594
CCDC163	MMACHC	Q9Y4U1	548
CCDC163	TMEM82	A0PJX8	530
CCDC163	SMIM10L2A	P0DMW4	506
CCDC163	DIP2C-AS1	Q8N8Z3	505
CCDC163	ARMCX4	Q5H9R4	474
CCDC163	TMEM69	Q5SWH9	448
CCDC163	GPBP1L1	Q9HC44	445
CCDC163	GPR15	P49685	438
CCDC163	WDR90	Q96KV7	390
CCDC163	MAP9	Q49MG5	376
CCDC163	LRATD2	Q96KN1	350
CCDC163	TESK2	Q96S53	336
CCDC163	ZFAND5	O76080	333
CCDC163	PRDX1	P35703	317

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0D9SF12, A2A8T7, A6H7E2, A6NF36, A6NFA0, A6NI87, E1C7U0, P03246, P03247, P0DO92, P14355, P14683, Q0VG49, Q1HVF6, Q32LN6, Q3KPU7, Q3KSS3, Q4V7D2, Q4ZG55, Q5DU28, Q5JX69, Q5JX71, Q5R7E2, Q5U4U4, Q642A3, Q6NRW0, Q6P1U0, Q6P4J6, Q6P9N1, Q6PEX7, Q6X4T0, Q7L3B6, Q7SYV9, Q7T346, Q80Y73, Q8BJS8, Q8CF25, Q8IWB6, Q8N6T0, Q8NCU1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

5 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	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1254 predictions. Top by Δscore:

Variant	Effect	Δscore
1:45495167:C:CC	acceptor_gain	1.0000
1:45496619:CTGGC:C	acceptor_gain	1.0000
1:45496622:GCC:G	acceptor_loss	1.0000
1:45496624:C:CA	acceptor_loss	1.0000
1:45496624:C:CC	acceptor_gain	1.0000
1:45496625:T:A	acceptor_loss	1.0000
1:45497297:A:AC	donor_gain	1.0000
1:45497298:C:CC	donor_gain	1.0000
1:45497298:CT:C	donor_gain	1.0000
1:45497298:CTCAA:C	donor_gain	1.0000
1:45497302:A:C	donor_gain	1.0000
1:45497384:C:CC	acceptor_gain	1.0000
1:45499441:CTG:C	acceptor_gain	1.0000
1:45499526:CCTCA:C	donor_loss	1.0000
1:45499527:CTCA:C	donor_loss	1.0000
1:45499528:TCA:T	donor_loss	1.0000
1:45499529:CA:C	donor_loss	1.0000
1:45499530:A:T	donor_loss	1.0000
1:45499531:C:CT	donor_loss	1.0000
1:45495162:GGGAT:G	acceptor_gain	0.9900
1:45495163:GGAT:G	acceptor_gain	0.9900
1:45495164:GAT:G	acceptor_gain	0.9900
1:45495165:AT:A	acceptor_gain	0.9900
1:45495544:TC:T	acceptor_gain	0.9900
1:45495545:CC:C	acceptor_gain	0.9900
1:45495546:CTG:C	acceptor_loss	0.9900
1:45495565:C:CT	acceptor_gain	0.9900
1:45495566:A:T	acceptor_gain	0.9900
1:45496340:TGGA:T	donor_gain	0.9900
1:45496550:TCCTA:T	donor_loss	0.9900

AlphaMissense

943 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:45495146:A:C	F117L	0.869
1:45495146:A:T	F117L	0.869
1:45495148:A:G	F117L	0.869
1:45497313:A:G	L83P	0.842
1:45497301:A:G	L87S	0.822
1:45499591:A:G	W7R	0.799
1:45499591:A:T	W7R	0.799
1:45495122:G:C	F125L	0.791
1:45495122:G:T	F125L	0.791
1:45495124:A:G	F125L	0.791
1:45499532:C:A	K26N	0.790
1:45499532:C:G	K26N	0.790
1:45499566:A:G	L15P	0.788
1:45497322:A:G	L80S	0.738
1:45499557:G:A	T18I	0.729
1:45496608:A:G	L93P	0.727
1:45499387:G:C	F45L	0.722
1:45499387:G:T	F45L	0.722
1:45499389:A:G	F45L	0.722
1:45499569:A:G	L14P	0.716
1:45499589:C:A	W7C	0.714
1:45499589:C:G	W7C	0.714
1:45497325:T:A	E79V	0.705
1:45499566:A:T	L15H	0.695
1:45497304:T:G	Q86P	0.682
1:45499539:C:G	R24P	0.682
1:45496559:C:A	W109C	0.670
1:45496559:C:G	W109C	0.670
1:45499578:A:G	L11P	0.670
1:45499378:G:C	S48R	0.668

dbSNP variants (sampled 300 via entrez): RS1001148146 (1:45500812 C>T), RS1001479218 (1:45493419 T>C), RS1001596498 (1:45500782 T>G), RS1002316208 (1:45501304 T>C), RS1002492767 (1:45493705 G>A), RS1002583955 (1:45501678 G>A), RS1002707657 (1:45497469 T>C,G), RS1002823547 (1:45495493 T>C), RS1003762112 (1:45495292 G>A,C,T), RS1003914379 (1:45500084 A>C,G), RS1005205241 (1:45496316 C>A,T), RS1005587567 (1:45501701 G>A), RS1005668891 (1:45495951 C>T), RS1005838616 (1:45494439 G>A), RS1005892621 (1:45496011 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

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
dicrotophos	increases expression	1
mono-(2-ethylhexyl)phthalate	affects expression, affects cotreatment	1
monobutyl phthalate	affects cotreatment, affects expression	1
hydroquinone	decreases expression	1
2-ethyl-5-carboxypentyl phthalate	affects cotreatment, affects expression	1
mono(2-ethyl-5-oxohexyl)phthalate	affects cotreatment, affects expression	1
mono-benzyl phthalate	affects cotreatment, affects expression	1
mono(2-ethyl-5-hydroxyhexyl) phthalate	affects cotreatment, affects expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
jinfukang	increases expression	1
mono-isobutyl phthalate	affects cotreatment, affects expression	1
monoethyl phthalate	affects cotreatment, affects expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	increases expression	1
Diuron	decreases expression	1
Valproic Acid	decreases methylation	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Particulate Matter	increases expression, increases abundance	1

Clinical trials (associated diseases)

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