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FLACC1 flagellum associated containing coiled-coil domains 1 [ Homo sapiens (human) ]

Gene ID: 130540, updated on 14-Nov-2024

Summary

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Official Symbol
FLACC1provided by HGNC
Official Full Name
flagellum associated containing coiled-coil domains 1provided by HGNC
Primary source
HGNC:HGNC:14439
See related
Ensembl:ENSG00000155749 MIM:619796; AllianceGenome:HGNC:14439
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
Also known as
ALS2CR12
Summary
Predicted to be located in cytoplasmic vesicle and outer dense fiber. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in testis (RPKM 8.4), lung (RPKM 1.1) and 3 other tissues See more
Orthologs
all
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Genomic context

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See FLACC1 in Genome Data Viewer
Location:
2q33.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (201288271..201364289, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (201768929..201844975, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (202152994..202222068, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene caspase 10 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:202084159-202084703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16982 Neighboring gene MT-ND4L pseudogene 13 Neighboring gene MT-ND4 pseudogene 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16986 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:202122995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16989 Neighboring gene caspase 8 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:202153225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:202184683-202185184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:202185185-202185684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16990 Neighboring gene trafficking kinesin protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:202289002-202289502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:202289503-202290003 Neighboring gene SCYL2 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:202315536-202316390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12232 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:202329405-202329904 Neighboring gene STE20 related adaptor beta

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Expression of a sperm flagellum component encoded by the Als2cr12 gene. Choi E, et al. Gene Expr Patterns, 2011 Jun-Jul. PMID 21402173
  2. Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk. Lin WY, et al. Hum Mol Genet, 2015 Jan 1. PMID 25168388, Free PMC Article
  3. New basal cell carcinoma susceptibility loci. Stacey SN, et al. Nat Commun, 2015 Apr 9. PMID 25855136, Free PMC Article
  4. Genome-wide association study identifies three new melanoma susceptibility loci. Barrett JH, et al. Nat Genet, 2011 Oct 9. PMID 21983787, Free PMC Article
  5. Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations. Wu C, et al. Nat Genet, 2014 Sep. PMID 25129146, Free PMC Article

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. rs13014235 is associated with susceptibility to cutaneous basal cell carcinoma.
    Title: New basal cell carcinoma susceptibility loci.
  2. Genome-wide association studies show a significant association between the intronic SNP rs1830298 in ALS2CR12 gene and breast cancer; further expression studies suggest that CASP8 might be the target gene.
    Title: Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk.
  3. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph.
  4. 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.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.
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
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
EBI GWAS Catalog
Genome-wide association study identifies three new melanoma susceptibility loci.
EBI GWAS Catalog
Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasmic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in outer dense fiber ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in sperm flagellum ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
flagellum-associated coiled-coil domain-containing protein 1
Names
ALS2 chromosome region 12
amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12
amyotrophic lateral sclerosis 2 chromosomal region candidate gene 12 protein
amyotrophic lateral sclerosis 2 chromosome region 12
amyotrophic lateral sclerosis 2 chromosome region candidate 12

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)

  1. NM_001127391.3 → NP_001120863.1  flagellum-associated coiled-coil domain-containing protein 1 isoform b

    See identical proteins and their annotated locations for NP_001120863.1

    Status: VALIDATED

    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 (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 encode the same protein (isoform b).
    Source sequence(s)
    AB053314, BC031603, BX095441, DB034999
    Consensus CDS
    CCDS46488.1
    UniProtKB/TrEMBL
    A8K8B8
    Related
    ENSP00000376086.3, ENST00000392257.8
    Conserved Domains (1) summary
    TIGR02168
    Location:113 → 393
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  2. NM_001289993.2 → NP_001276922.1  flagellum-associated coiled-coil domain-containing protein 1 isoform b

    See identical proteins and their annotated locations for NP_001276922.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 encode the same protein (isoform b).
    Source sequence(s)
    AB053314, AC007256, AK292283
    Consensus CDS
    CCDS46488.1
    UniProtKB/TrEMBL
    A8K8B8
    Related
    ENSP00000412073.1, ENST00000439709.5
    Conserved Domains (1) summary
    TIGR02168
    Location:113 → 393
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  3. NM_139163.4 → NP_631902.2  flagellum-associated coiled-coil domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_631902.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AB053314, AC007256, CD703925, DB054409
    Consensus CDS
    CCDS2346.1
    UniProtKB/Swiss-Prot
    G5E9S3, Q53TT6, Q8N1B6, Q96Q35
    UniProtKB/TrEMBL
    A8K8B8
    Related
    ENSP00000385098.2, ENST00000405148.6
    Conserved Domains (1) summary
    TIGR02169
    Location:117 → 399
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

RNA

  1. NR_110620.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB053314, AC007256, AK124115, CD703925, DB054409
    Related
    ENST00000494171.5

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    201288271..201364289 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452696.2 → XP_024308464.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    G5E9S3, Q53TT6, Q8N1B6, Q96Q35
    UniProtKB/TrEMBL
    A8K8B8
    Conserved Domains (1) summary
    TIGR02169
    Location:117 → 399
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

  2. XM_047443393.1 → XP_047299349.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X3

  3. XM_011510606.4 → XP_011508908.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    A8K8B8
    Conserved Domains (1) summary
    TIGR02168
    Location:127 → 361
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  4. XM_047443395.1 → XP_047299351.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X4

  5. XM_047443394.1 → XP_047299350.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X4

  6. XM_011510610.4 → XP_011508912.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X5

  7. XM_011510612.4 → XP_011508914.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X7

  8. XM_047443396.1 → XP_047299352.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    201768929..201844975 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054340534.1 → XP_054196509.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X1

  2. XM_054340536.1 → XP_054196511.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X3

  3. XM_054340535.1 → XP_054196510.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X2

  4. XM_054340538.1 → XP_054196513.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X4

  5. XM_054340537.1 → XP_054196512.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X4

  6. XM_054340539.1 → XP_054196514.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X5

  7. XM_054340541.1 → XP_054196516.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X7

  8. XM_054340540.1 → XP_054196515.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96Q35.2 GenPept UniProtKB/Swiss-Prot:Q96Q35

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