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CFAP410 cilia and flagella associated protein 410 [ Homo sapiens (human) ]

Gene ID: 755, updated on 27-Nov-2024

Summary

Official Symbol
CFAP410provided by HGNC
Official Full Name
cilia and flagella associated protein 410provided by HGNC
Primary source
HGNC:HGNC:1260
See related
Ensembl:ENSG00000160226 MIM:603191; AllianceGenome:HGNC:1260
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
RDMS; SMDAX; LRRC76; YF5/A2; C21orf2
Summary
Four alternatively spliced transcript variants encoding four different isoforms have been found for this nuclear gene. All isoforms contain leucine-rich repeats. Three of these isoforms are mitochondrial proteins and one of them lacks the target peptide, so is not located in mitochondrion. This gene is down-regulated in Down syndrome (DS) brain, which may represent mitochondrial dysfunction in DS patients. [provided by RefSeq, Sep 2012]
Expression
Ubiquitous expression in kidney (RPKM 7.1), spleen (RPKM 5.4) and 25 other tissues See more
Orthologs
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Genomic context

See CFAP410 in Genome Data Viewer
Location:
21q22.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44328944..44339390, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42683001..42693484, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45748827..45759273, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18568 Neighboring gene autoimmune regulator Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45724667-45725466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45725506-45726160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45726161-45726814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45727470-45728123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13381 Neighboring gene phosphofructokinase, liver type Neighboring gene Sharpr-MPRA regulatory region 3786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18569 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45751251-45751752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45751753-45752252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13383 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr21:45761314-45761956 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr21:45761957-45762600 Neighboring gene NANOG hESC enhancer GRCh37_chr21:45763343-45763898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45765021-45765523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18572 Neighboring gene transient receptor potential cation channel subfamily M member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45790067-45790900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45797213-45797712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45797713-45798214 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45798708-45798913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45821987-45822910 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:45825427-45826626 Neighboring gene TRPM2 antisense RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18573 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45846369-45847280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45847281-45848192 Neighboring gene Z6 small nucleolar RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45857057-45857556

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • AP001062.8

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IEA
Inferred from Electronic Annotation
more info
 
involved_in cilium assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of cell shape IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
located_in photoreceptor connecting cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in photoreceptor outer segment IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
cilia- and flagella-associated protein 410; nuclear encoded mitochondrial protein C21orf2
Names
C21orf-HUMF09G8.5
leucine rich repeat containing 76
leucine-rich repeat-containing protein 76
protein C21orf2

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

  1. NG_032952.1 RefSeqGene

    Range
    5013..15459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001271440.2NP_001258369.1  nuclear encoded mitochondrial protein C21orf2 isoform 2

    See identical proteins and their annotated locations for NP_001258369.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2, also known as YF5) lacks an internal aa, compared to isoform 1.
    Source sequence(s)
    BM761336, U84569, Y11392
    Consensus CDS
    CCDS59445.1
    Related
    ENSP00000317302.7, ENST00000325223.7
    Conserved Domains (4) summary
    smart00446
    Location:104122
    LRRcap; occurring C-terminal to leucine-rich repeats
    sd00035
    Location:4263
    LRR_NTF; leucine-rich repeat [structural motif]
    pfam12799
    Location:4080
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:1974
    LRR_8; Leucine rich repeat
  2. NM_001271441.2NP_001258370.1  nuclear encoded mitochondrial protein C21orf2 isoform 3

    See identical proteins and their annotated locations for NP_001258370.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (3) has an additional segment in the C-terminal region, compared to isoform 1.
    Source sequence(s)
    BC031300, Y11392
    Consensus CDS
    CCDS59444.1
    UniProtKB/Swiss-Prot
    O43822
    Related
    ENSP00000381047.3, ENST00000397956.7
    Conserved Domains (4) summary
    smart00446
    Location:104122
    LRRcap; occurring C-terminal to leucine-rich repeats
    sd00035
    Location:4263
    LRR_NTF; leucine-rich repeat [structural motif]
    pfam12799
    Location:4080
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:1974
    LRR_8; Leucine rich repeat
  3. NM_001271442.1NP_001258371.1  cilia- and flagella-associated protein 410 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate 5' exon and an additional exon in the 5' region, which cause translation initiation at a downstream AUG, compared to variant 1. The resulting isoform (4, also known as A2) is shorter and lacks a mitochondrial targeting peptide, compared to isoform 1.
    Source sequence(s)
    AP001062, BC031300, U84570, Y11392
    Conserved Domains (3) summary
    smart00446
    Location:6381
    LRRcap; occurring C-terminal to leucine-rich repeats
    sd00035
    Location:2346
    LRR_NTF; leucine-rich repeat [structural motif]
    pfam12799
    Location:239
    LRR_4; Leucine Rich repeats (2 copies)
  4. NM_004928.3NP_004919.1  nuclear encoded mitochondrial protein C21orf2 isoform 1

    See identical proteins and their annotated locations for NP_004919.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes a mitochondrial protein (isoform 1).
    Source sequence(s)
    BC072012, BM761336, Y11392
    Consensus CDS
    CCDS13709.1
    UniProtKB/Swiss-Prot
    A8MPS9, O14993, O43822, Q8N5X6, Q99837, Q99838
    Related
    ENSP00000344566.4, ENST00000339818.9
    Conserved Domains (4) summary
    smart00446
    Location:104122
    LRRcap; occurring C-terminal to leucine-rich repeats
    sd00035
    Location:4263
    LRR_NTF; leucine-rich repeat [structural motif]
    pfam12799
    Location:4080
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:1974
    LRR_8; Leucine rich repeat

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

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    44328944..44339390 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047440986.1XP_047296942.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

  2. XM_047440982.1XP_047296938.1  nuclear encoded mitochondrial protein C21orf2 isoform X3

  3. XM_047440981.1XP_047296937.1  nuclear encoded mitochondrial protein C21orf2 isoform X2

  4. XM_047440980.1XP_047296936.1  nuclear encoded mitochondrial protein C21orf2 isoform X1

  5. XM_047440983.1XP_047296939.1  nuclear encoded mitochondrial protein C21orf2 isoform X5

  6. XM_006724051.4XP_006724114.1  nuclear encoded mitochondrial protein C21orf2 isoform X4

    Conserved Domains (3) summary
    smart00446
    Location:129147
    LRRcap; occurring C-terminal to leucine-rich repeats
    sd00035
    Location:89112
    LRR_NTF; leucine-rich repeat [structural motif]
    pfam12799
    Location:87123
    LRR_4; Leucine Rich repeats (2 copies)
  7. XM_047440987.1XP_047296943.1  nuclear encoded mitochondrial protein C21orf2 isoform X7

  8. XM_047440984.1XP_047296940.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

  9. XM_047440985.1XP_047296941.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    42683001..42693484 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324849.1XP_054180824.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

  2. XM_054324844.1XP_054180819.1  nuclear encoded mitochondrial protein C21orf2 isoform X3

  3. XM_054324843.1XP_054180818.1  nuclear encoded mitochondrial protein C21orf2 isoform X2

  4. XM_054324842.1XP_054180817.1  nuclear encoded mitochondrial protein C21orf2 isoform X1

  5. XM_054324846.1XP_054180821.1  nuclear encoded mitochondrial protein C21orf2 isoform X5

  6. XM_054324845.1XP_054180820.1  nuclear encoded mitochondrial protein C21orf2 isoform X4

  7. XM_054324850.1XP_054180825.1  nuclear encoded mitochondrial protein C21orf2 isoform X7

  8. XM_054324847.1XP_054180822.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

  9. XM_054324848.1XP_054180823.1  nuclear encoded mitochondrial protein C21orf2 isoform X6