CCDC38 coiled-coil domain containing 38 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCDC38provided by HGNC
Official Full Name: coiled-coil domain containing 38provided by HGNC
Primary source: HGNC:HGNC:26843
See related: Ensembl:ENSG00000165972 AllianceGenome:HGNC:26843
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Predicted to enable ubiquitin-modified histone reader activity. Predicted to be involved in acrosome assembly and sperm flagellum assembly. Located in centrosome. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Restricted expression toward testis (RPKM 5.9) See more
Orthologs: mouse all
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Genomic context

Location:: 12q23.1

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (95867048..95943233, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (95843468..95919803, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (96260826..96336392, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

strongest signal of association with smoking resistance for a non-synonymous SNP in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells
Title: Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ubiquitin-modified histone reader activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in acrosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in intraciliary anterograde transport	IEA Inferred from Electronic Annotation more info
involved_in sperm flagellum assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in manchette	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in sperm flagellum	IEA Inferred from Electronic Annotation more info
located_in sperm head	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: coiled-coil domain-containing protein 38

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.

mRNA and Protein(s)

NM_182496.3 → NP_872302.2 coiled-coil domain-containing protein 38

See identical proteins and their annotated locations for NP_872302.2

Status: VALIDATED

Source sequence(s)

AK097408, BC095479

Consensus CDS

CCDS9056.1

UniProtKB/Swiss-Prot

Q502W7, Q8N835

Related

ENSP00000345470.3, ENST00000344280.8

Conserved Domains (1) summary

pfam13863
Location:112 → 230

DUF4200; Domain of unknown function (DUF4200)

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_000012.12 Reference GRCh38.p14 Primary Assembly

Range

95867048..95943233 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011537883.3 → XP_011536185.1 coiled-coil domain-containing protein 38 isoform X1

See identical proteins and their annotated locations for XP_011536185.1

UniProtKB/Swiss-Prot

Q502W7, Q8N835

Conserved Domains (1) summary

pfam13863
Location:112 → 230

DUF4200; Domain of unknown function (DUF4200)
XM_047428281.1 → XP_047284237.1 coiled-coil domain-containing protein 38 isoform X2
XM_011537888.4 → XP_011536190.1 coiled-coil domain-containing protein 38 isoform X3
XM_011537889.2 → XP_011536191.1 coiled-coil domain-containing protein 38 isoform X4

Conserved Domains (1) summary

pfam13863
Location:112 → 230

DUF4200; Domain of unknown function (DUF4200)

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

95843468..95919803 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054371059.1 → XP_054227034.1 coiled-coil domain-containing protein 38 isoform X1
XM_054371060.1 → XP_054227035.1 coiled-coil domain-containing protein 38 isoform X2
XM_054371061.1 → XP_054227036.1 coiled-coil domain-containing protein 38 isoform X3
XM_054371062.1 → XP_054227037.1 coiled-coil domain-containing protein 38 isoform X4