CC2D1A coiled-coil and C2 domain containing 1A [Homo sapiens (human)] - Gene

Summary

Official Symbol: CC2D1Aprovided by HGNC
Official Full Name: coiled-coil and C2 domain containing 1Aprovided by HGNC
Primary source: HGNC:HGNC:30237
See related: Ensembl:ENSG00000132024 MIM:610055; AllianceGenome:HGNC:30237
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: Lgd2; MRT3; TAPE; Aki-1; FREUD-1; Freud-1/Aki1
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 of the protein are inhibited by calcium. A mutation in this gene results in a nonsyndromic form of cognitive disability (MRT3). [provided by RefSeq, Jul 2017]
Expression: Ubiquitous expression in duodenum (RPKM 16.8), small intestine (RPKM 12.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.12

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (13906201..13930879)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (14032358..14057039)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (14017014..14041692)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow.
Title: CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow.
Effects of the Cc2d1a/Freud-1 Knockdown in the Hippocampus of BTBR Mice on the Autistic-Like Behavior, Expression of Serotonin 5-HT1A and D2 Dopamine Receptors, and CREB and NF-kB Intracellular Signaling.
Title: Effects of the Cc2d1a/Freud-1 Knockdown in the Hippocampus of BTBR Mice on the Autistic-Like Behavior, Expression of Serotonin 5-HT(1A) and D2 Dopamine Receptors, and CREB and NF-kB Intracellular Signaling.
Novel alterations of CC2D1A as a candidate gene in a Turkish sample of patients with autism spectrum disorder.
Title: Novel alterations of CC2D1A as a candidate gene in a Turkish sample of patients with autism spectrum disorder.
Monoallelic Mutations in CC2D1A Suggest a Novel Role in Human Heterotaxy and Ciliary Dysfunction.
Title: Monoallelic Mutations in CC2D1A Suggest a Novel Role in Human Heterotaxy and Ciliary Dysfunction.
Unravelling of Hidden Secrets: The Tumour Suppressor Lethal (2) Giant Discs (Lgd)/CC2D1, Notch Signalling and Cancer.
Title: Unravelling of Hidden Secrets: The Tumour Suppressor Lethal (2) Giant Discs (Lgd)/CC2D1, Notch Signalling and Cancer.
Both expressions of CC2D1A and HTR1A genes studied on autism spectrum disorder cases and controls were significantly different
Title: The roles of CC2D1A and HTR1A gene expressions in autism spectrum disorders.
CC2D1A binds to CHMP4B polymers formed on endosomes to regulate the endosomal sorting pathway.CC2D1A regulates degradation and signaling of EGFR and TLR4.
Title: CC2D1A and CC2D1B regulate degradation and signaling of EGFR and TLR4.
Aki1 was expressed in human diffuse malignant mesothelioma specimens. Expression correlated with phosphorylated CREB1. Aki1 regulates CREB by modulating protein kinase A activity. The Aki1-CREB axis plays an important role in DMM pathogenesis.
Title: Akt Kinase-Interacting Protein 1 Signals through CREB to Drive Diffuse Malignant Mesothelioma.
Null mutations in CC2D1A consistently cause a variable spectrum of presentations including ID, ASD, and seizures. CC2D1A regulates NF-kappaB signaling.
Title: CC2D1A regulates human intellectual and social function as well as NF-κB signaling homeostasis.
All of the pancreatic cancer cell lines expressed Aki1. Silencing of Aki1 in Panc1 cells reduced the phosphorylation of Akt and increased the phosphorylation of cleaved PARP.
Title: Expression of Akt kinase-interacting protein 1, a scaffold protein of the PI3K/PDK1/Akt pathway, in pancreatic cancer.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual disability, autosomal recessive 3 MedGen: C1838023 OMIM: 608443 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
retropepsin	gag-pol	Positional proteomics analysis identifies the cleavage of human coiled-coil and C2 domain containing 1A (CC2D1A) at amino acid residues 783-784 by the HIV-1 protease	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

GDB:313557 (e-PCR)
- UniSTS:8230

sY3084 (e-PCR)
- UniSTS:515126

D19S840 (e-PCR), detects polymorphism
- UniSTS:17720

RH104325 (e-PCR)
- UniSTS:98650

RH80706 (e-PCR)
- UniSTS:90621

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables cadherin binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in apical dendrite arborization	IEA Inferred from Electronic Annotation more info
involved_in endosome organization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of snRNA transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of canonical NF-kappaB signal transduction	HMP more info	PubMed
involved_in regulation of postsynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of respiratory gaseous exchange by nervous system process	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: coiled-coil and C2 domain-containing protein 1A

Names: Akt kinase-interacting protein 1; FRE under dual repression-binding protein 1; TBK1-associated protein in endolysosomes; five prime repressor element under dual repression-binding protein 1; five repressor element under dual repression-binding protein 1; lethal (2) giant discs homolog 2; putative NF-kappa-B-activating protein 023N; putative NFkB activating protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_013089.1 RefSeqGene

Range

5059..29737

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001411138.1 → NP_001398067.1 coiled-coil and C2 domain-containing protein 1A isoform 2

Status: REVIEWED

Source sequence(s)

AC020916

Consensus CDS

CCDS92537.1

Related

ENSP00000467526.1, ENST00000589606.5
NM_017721.5 → NP_060191.3 coiled-coil and C2 domain-containing protein 1A isoform 1

See identical proteins and their annotated locations for NP_060191.3

Status: REVIEWED

Source sequence(s)

BC064981, DB065701

Consensus CDS

CCDS42512.1

UniProtKB/Swiss-Prot

Q6P1N0, Q7Z435, Q86XV0, Q8NF89, Q9H603, Q9NXI1

Related

ENSP00000313601.6, ENST00000318003.11

Conserved Domains (2) summary

smart00685
Location:349 → 407

DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241

cd08690
Location:652 → 809

C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

13906201..13930879

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439012.1 → XP_047294968.1 coiled-coil and C2 domain-containing protein 1A isoform X1
XM_047439014.1 → XP_047294970.1 coiled-coil and C2 domain-containing protein 1A isoform X2
XM_047439015.1 → XP_047294971.1 coiled-coil and C2 domain-containing protein 1A isoform X3
XM_047439017.1 → XP_047294973.1 coiled-coil and C2 domain-containing protein 1A isoform X5
XM_047439016.1 → XP_047294972.1 coiled-coil and C2 domain-containing protein 1A isoform X4
XM_047439018.1 → XP_047294974.1 coiled-coil and C2 domain-containing protein 1A isoform X6
XM_047439019.1 → XP_047294975.1 coiled-coil and C2 domain-containing protein 1A isoform X7

UniProtKB/TrEMBL

A0A7P0Z4M5
XM_047439020.1 → XP_047294976.1 coiled-coil and C2 domain-containing protein 1A isoform X8

UniProtKB/TrEMBL

A0A7P0Z4M5

Related

ENSP00000506358.1, ENST00000680977.1

Reference GRCh38.p14 PATCHES

Genomic

NW_021160022.1 Reference GRCh38.p14 PATCHES

Range

118042..142720

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054332691.1 → XP_054188666.1 coiled-coil and C2 domain-containing protein 1A isoform X1
XM_054332692.1 → XP_054188667.1 coiled-coil and C2 domain-containing protein 1A isoform X2
XM_054332693.1 → XP_054188668.1 coiled-coil and C2 domain-containing protein 1A isoform X3
XM_054332695.1 → XP_054188670.1 coiled-coil and C2 domain-containing protein 1A isoform X5
XM_054332694.1 → XP_054188669.1 coiled-coil and C2 domain-containing protein 1A isoform X4
XM_054332696.1 → XP_054188671.1 coiled-coil and C2 domain-containing protein 1A isoform X6
XM_054332697.1 → XP_054188672.1 coiled-coil and C2 domain-containing protein 1A isoform X7

UniProtKB/TrEMBL

A0A7P0Z4M5
XM_054332698.1 → XP_054188673.1 coiled-coil and C2 domain-containing protein 1A isoform X8

UniProtKB/TrEMBL

A0A7P0Z4M5

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

14032358..14057039

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054321331.1 → XP_054177306.1 coiled-coil and C2 domain-containing protein 1A isoform X1
XM_054321332.1 → XP_054177307.1 coiled-coil and C2 domain-containing protein 1A isoform X2
XM_054321333.1 → XP_054177308.1 coiled-coil and C2 domain-containing protein 1A isoform X3
XM_054321335.1 → XP_054177310.1 coiled-coil and C2 domain-containing protein 1A isoform X5
XM_054321334.1 → XP_054177309.1 coiled-coil and C2 domain-containing protein 1A isoform X4
XM_054321336.1 → XP_054177311.1 coiled-coil and C2 domain-containing protein 1A isoform X6
XM_054321337.1 → XP_054177312.1 coiled-coil and C2 domain-containing protein 1A isoform X7

UniProtKB/TrEMBL

A0A7P0Z4M5
XM_054321338.1 → XP_054177313.1 coiled-coil and C2 domain-containing protein 1A isoform X8

UniProtKB/TrEMBL

A0A7P0Z4M5