CC2D1A (coiled-coil and C2 domain containing 1A)

Gene

• Entrez ID: 54862
• Gene name: Coiled-coil and C2 domain containing 1A
• Gene symbol: CC2D1A
• Synonyms (NCBI Gene): Aki-1, FREUD-1, Freud-1/Aki1, Lgd2, MRT3, TAPE
• Chromosome: 19
• Chromosome location: 19p13.12
• Summary: This gene encodes a transcriptional repressor that binds to a conserved 14-bp 5`-repressor element and regulates expression of the 5-hydroxytryptamine (serotonin) receptor 1A gene in neuronal cells. The DNA binding and transcriptional repressor activities

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs34146052	G>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs201177183	G>A,C,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs201921029	G>A	Pathogenic, benign, uncertain-significance	Missense variant, coding sequence variant
rs202057391	C>T	Pathogenic, conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance, benign	Missense variant, coding sequence variant
rs541952457	TGGGCAG>-	Conflicting-interpretations-of-pathogenicity	Intron variant
rs754855261	C>A,T	Likely-pathogenic	Synonymous variant, stop gained, coding sequence variant
rs876657679	G>T	Pathogenic	Splice donor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT440995	hsa-miR-485-5p	HITS-CLIP	24374217
MIRT440994	hsa-miR-377-5p	HITS-CLIP	24374217
MIRT150380	hsa-miR-19a-3p	HITS-CLIP	22473208
MIRT150381	hsa-miR-19b-3p	HITS-CLIP	22473208
MIRT440995	hsa-miR-485-5p	HITS-CLIP	24374217
MIRT440994	hsa-miR-377-5p	HITS-CLIP	24374217
MIRT866958	hsa-miR-1255a	CLIP-seq
MIRT866959	hsa-miR-1255b	CLIP-seq
MIRT866960	hsa-miR-1538	CLIP-seq
MIRT866961	hsa-miR-1908	CLIP-seq
MIRT866962	hsa-miR-198	CLIP-seq
MIRT866963	hsa-miR-2467-5p	CLIP-seq
MIRT866964	hsa-miR-3150a-3p	CLIP-seq
MIRT866965	hsa-miR-3170	CLIP-seq
MIRT866966	hsa-miR-3175	CLIP-seq
MIRT866967	hsa-miR-3184	CLIP-seq
MIRT866968	hsa-miR-3194-5p	CLIP-seq
MIRT866969	hsa-miR-331-3p	CLIP-seq
MIRT866970	hsa-miR-342-5p	CLIP-seq
MIRT866971	hsa-miR-423-5p	CLIP-seq
MIRT866972	hsa-miR-4260	CLIP-seq
MIRT866973	hsa-miR-4292	CLIP-seq
MIRT866974	hsa-miR-4302	CLIP-seq
MIRT866975	hsa-miR-4474-3p	CLIP-seq
MIRT866976	hsa-miR-4488	CLIP-seq
MIRT866977	hsa-miR-4492	CLIP-seq
MIRT866978	hsa-miR-4498	CLIP-seq
MIRT866979	hsa-miR-4505	CLIP-seq
MIRT866980	hsa-miR-4508	CLIP-seq
MIRT866981	hsa-miR-4651	CLIP-seq
MIRT866982	hsa-miR-4664-5p	CLIP-seq
MIRT866983	hsa-miR-4667-5p	CLIP-seq
MIRT866984	hsa-miR-4691-3p	CLIP-seq
MIRT866985	hsa-miR-4697-5p	CLIP-seq
MIRT866986	hsa-miR-4700-5p	CLIP-seq
MIRT866987	hsa-miR-4731-5p	CLIP-seq
MIRT866988	hsa-miR-4745-3p	CLIP-seq
MIRT866989	hsa-miR-608	CLIP-seq
MIRT866990	hsa-miR-637	CLIP-seq
MIRT866991	hsa-miR-644	CLIP-seq
MIRT866992	hsa-miR-663	CLIP-seq
MIRT866993	hsa-miR-744	CLIP-seq
MIRT866994	hsa-miR-760	CLIP-seq
MIRT866995	hsa-miR-762	CLIP-seq
MIRT866996	hsa-miR-9	CLIP-seq
MIRT866997	hsa-miR-939	CLIP-seq
MIRT1957287	hsa-miR-1231	CLIP-seq
MIRT1957288	hsa-miR-4288	CLIP-seq
MIRT1957289	hsa-miR-4640-5p	CLIP-seq
MIRT1957290	hsa-miR-4726-5p	CLIP-seq
MIRT1957291	hsa-miR-632	CLIP-seq
MIRT2194262	hsa-miR-1207-3p	CLIP-seq
MIRT2194263	hsa-miR-1262	CLIP-seq
MIRT2194264	hsa-miR-1286	CLIP-seq
MIRT2194265	hsa-miR-1291	CLIP-seq
MIRT2194266	hsa-miR-3144-5p	CLIP-seq
MIRT866964	hsa-miR-3150a-3p	CLIP-seq
MIRT2194267	hsa-miR-3158-3p	CLIP-seq
MIRT866965	hsa-miR-3170	CLIP-seq
MIRT866966	hsa-miR-3175	CLIP-seq
MIRT866967	hsa-miR-3184	CLIP-seq
MIRT2194268	hsa-miR-3191	CLIP-seq
MIRT866969	hsa-miR-331-3p	CLIP-seq
MIRT866970	hsa-miR-342-5p	CLIP-seq
MIRT2194269	hsa-miR-3928	CLIP-seq
MIRT866971	hsa-miR-423-5p	CLIP-seq
MIRT866972	hsa-miR-4260	CLIP-seq
MIRT866973	hsa-miR-4292	CLIP-seq
MIRT2194270	hsa-miR-4459	CLIP-seq
MIRT866979	hsa-miR-4505	CLIP-seq
MIRT1957289	hsa-miR-4640-5p	CLIP-seq
MIRT2194271	hsa-miR-4650-5p	CLIP-seq
MIRT866981	hsa-miR-4651	CLIP-seq
MIRT2194272	hsa-miR-4652-5p	CLIP-seq
MIRT866982	hsa-miR-4664-5p	CLIP-seq
MIRT866983	hsa-miR-4667-5p	CLIP-seq
MIRT2194273	hsa-miR-4688	CLIP-seq
MIRT866986	hsa-miR-4700-5p	CLIP-seq
MIRT2194274	hsa-miR-4701-3p	CLIP-seq
MIRT2194275	hsa-miR-4710	CLIP-seq
MIRT2194276	hsa-miR-4721	CLIP-seq
MIRT2194277	hsa-miR-4722-5p	CLIP-seq
MIRT1957290	hsa-miR-4726-5p	CLIP-seq
MIRT866987	hsa-miR-4731-5p	CLIP-seq
MIRT2194278	hsa-miR-4779	CLIP-seq
MIRT866989	hsa-miR-608	CLIP-seq
MIRT2194279	hsa-miR-661	CLIP-seq
MIRT2194280	hsa-miR-711	CLIP-seq
MIRT866996	hsa-miR-9	CLIP-seq
MIRT866997	hsa-miR-939	CLIP-seq
MIRT2194265	hsa-miR-1291	CLIP-seq
MIRT2194266	hsa-miR-3144-5p	CLIP-seq
MIRT866964	hsa-miR-3150a-3p	CLIP-seq
MIRT866966	hsa-miR-3175	CLIP-seq
MIRT2194268	hsa-miR-3191	CLIP-seq
MIRT2385595	hsa-miR-328	CLIP-seq
MIRT2194269	hsa-miR-3928	CLIP-seq
MIRT866973	hsa-miR-4292	CLIP-seq
MIRT866979	hsa-miR-4505	CLIP-seq
MIRT2194272	hsa-miR-4652-5p	CLIP-seq
MIRT866983	hsa-miR-4667-5p	CLIP-seq
MIRT866986	hsa-miR-4700-5p	CLIP-seq
MIRT2385596	hsa-miR-4716-5p	CLIP-seq
MIRT866987	hsa-miR-4731-5p	CLIP-seq
MIRT2194280	hsa-miR-711	CLIP-seq
MIRT866997	hsa-miR-939	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	12917378
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA	12917378
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0001650	Component	Fibrillar center	IDA
GO:0002087	Process	Regulation of respiratory gaseous exchange by nervous system process	IEA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	16730941, 26496610, 35271311
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IDA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007032	Process	Endosome organization	IEA
GO:0010008	Component	Endosome membrane	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0036064	Component	Ciliary basal body	IDA
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	HMP	12761501
GO:0043576	Process	Regulation of respiratory gaseous exchange	IEA
GO:0045202	Component	Synapse	IEA
GO:0045296	Function	Cadherin binding	HDA	25468996
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0140059	Process	Dendrite arborization	IEA
GO:0150023	Process	Apical dendrite arborization	IEA
GO:0150052	Process	Regulation of postsynapse assembly	IEA
GO:1905381	Process	Negative regulation of snRNA transcription by RNA polymerase II	IDA	12917378

Other IDs

• MIM: 610055
• HGNC: 30237
• e!Ensembl: ENSG00000132024

Protein

• UniProt ID: Q6P1N0
• Protein name: Coiled-coil and C2 domain-containing protein 1A (Akt kinase-interacting protein 1) (Five prime repressor element under dual repression-binding protein 1) (FRE under dual repression-binding protein 1) (Freud-1) (Putative NF-kappa-B-activating protein 023N)
• Protein function: Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells. The combination of calcium and ATP specifically inactivates the binding with FRE. May play a role in the a
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00168	C2	655 → 772	C2 domain	Domain

• Sequence:

  MHKRKGPPGPPGRGAAAARQLGLLVDLSPDGLMIPEDGANDEELEAEFLALVGGQPPALE
  KLKGKGPLPMEAIEKMASLCMRDPDEDEEEGTDEDDLEADDDLLAELNEVLGEEQKASET
  PPPVAQPKPEAPHPGLETTLQERLALYQTAIESARQAGDSAKMRRYDRGLKTLENLLASI
  RKGNAIDEADIPPPVAIGKGPASTPTYSPAPTQPAPRIASAPEPRVTLEGPSATAPASSP
  GLAKPQMPPGPCSPGPLAQLQSRQRDYKLAALHAKQQGDTTAAARHFRVAKSFDAVLEAL
  SRGEPVDLSCLPPPPDQLPPDPPSPPSQPPTPATAPSTTEVPPPPRTLLEALEQRMERYQ
  VAAAQAKSKGDQRKARMHERIVKQYQDAIRAHKAGRAVDVAELPVPPGFPPIQGLEATKP
  TQQSLVGVLETAMKLANQDEGPEDEEDEVPKKQNSPVAPTAQPKAPPSRTPQSGSAPTAK
  APPKATSTRAQQQLAFLEGRKKQLLQAALRAKQKNDVEGAKMHLRQAKGLEPMLEASRNG
  LPVDITKVPPAPVNKDDFALVQRPGPGLSQEAARRYGELTKLIRQQHEMCLNHSNQFTQL
  GNITETTKFEKLAEDCKRSMDILKQAFVRGLPTPTARFEQRTFSVIKIFPDLSSNDMLLF
  IVKGINLPTPPGLSPGDLDVFVRFDFPYPNVEEAQKDKTSVIKNTDSPEFKEQFKLCINR
  SHRGFRRAIQTKGIKFEVVHKGGLFKTDRVLGTAQLKLDALEIACEVREILEVLDGRRPT
  GGRLEVMVRIREPLTAQQLETTTERWLVIDPVPAAVPTQVAGPKGKAPPVPAPARESGNR
  SARPLHSLSVLAFDQERLERKILALRQARRPVPPEVAQQYQDIMQRSQWQRAQLEQGGVG
  IRREYAAQLERQLQFYTEAARRLGNDGSRDAAKEALYRRNLVESELQRLRR

• Sequence length: 951

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Autosomal recessive non-syndromic intellectual disability	Pathogenic	rs779620838	RCV002272954
Clear cell carcinoma of kidney	Likely pathogenic	rs200450636	RCV005931856
Colon adenocarcinoma	Likely pathogenic	rs1971662595	RCV005930045
Intellectual disability, autosomal recessive 3	Pathogenic; Likely pathogenic	rs2145350143, rs777057767, rs200450636, rs2513094283, rs1970938126, rs2513147217, rs2513150660, rs1971392241, rs1423002835	RCV001780452 RCV001780723 RCV002509834 RCV005030130 RCV005030173 RCV005030322 RCV003988785 RCV001262582 RCV001264805

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
CC2D1A-related disorder	Benign; Conflicting classifications of pathogenicity; Likely benign; Uncertain significance	rs11883041, rs202057391, rs61740117, rs200121704, rs760486441, rs202106696, rs191830054, rs143529486, rs797045435, rs147905122, rs201251295, rs77389229, rs747892591, rs371243328, rs375094506, rs1252107252, rs557346390, rs373165331, rs201404472, rs73922801, rs56359259, rs769120532, rs376336714, rs529368098, rs73925404, rs200354654, rs35337537, rs199717745, rs80078962, rs372760536, rs201853183, rs187912873	RCV003975009 RCV003915140 RCV003915141 RCV003964977 RCV003896127 RCV003903689 RCV003917738 RCV003947600 RCV004757157 RCV003967494 RCV003937685 RCV003927770 RCV004757596 RCV003909019 RCV003954273 RCV003929278 RCV003956465 RCV003939179 RCV003893338 RCV003957897 RCV003950338 RCV003902762 RCV003925452 RCV003960154 RCV003960155 RCV003915365 RCV003953273 RCV003948381 RCV003940576 RCV003910818 RCV003932937 RCV003902895 RCV003933001
Cervical cancer	Conflicting classifications of pathogenicity	rs201251295	RCV005892260
Familial cancer of breast	Conflicting classifications of pathogenicity	rs200557641	RCV005901848
Gastric cancer	-	rs780010188	RCV005930103
Intellectual disability	Conflicting classifications of pathogenicity; Benign	rs143529486, rs201884654, rs201251295, rs3217680	RCV001252185 RCV001252184 RCV001252183 RCV001252182
Malignant lymphoma, large B-cell, diffuse	Conflicting classifications of pathogenicity	rs201251295	RCV005892262
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	rs200557641, rs77389229	RCV005901849 RCV005902962
Melanoma	Conflicting classifications of pathogenicity	rs201251295	RCV005892263
Smith-Magenis Syndrome-like	Conflicting classifications of pathogenicity	rs202057391, rs201921029	RCV000491268 RCV000491719
Uterine corpus endometrial carcinoma	Conflicting classifications of pathogenicity	rs192358667	RCV005899837
Uveal melanoma	Conflicting classifications of pathogenicity	rs201251295	RCV005892261

Associations from Text Mining
Disease Name	Relationship Type	References
Agenesis of Cerebellar Vermis	Associate	34205586
Cerebral Palsy	Associate	34580524
Intellectual Disability	Associate	16033914, 20529849, 22419660, 27914010, 30500859, 34580524
Mental Disorders	Associate	22328058
Mental Retardation Autosomal Recessive 4	Associate	16033914, 34580524
Mental Retardation X Linked Nonsyndromic	Associate	18452889, 34205586
Psychological Trauma	Associate	34580524