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    SPEF2 sperm flagellar 2 [ Homo sapiens (human) ]

    Gene ID: 79925, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SPEF2provided by HGNC
    Official Full Name
    sperm flagellar 2provided by HGNC
    Primary source
    HGNC:HGNC:26293
    See related
    Ensembl:ENSG00000152582 MIM:610172; AllianceGenome:HGNC:26293
    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
    KPL2; CT122; SPGF43
    Summary
    Involved in sperm axoneme assembly. Located in sperm flagellum. Implicated in spermatogenic failure 43. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in endometrium (RPKM 2.4), testis (RPKM 2.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPEF2 in Genome Data Viewer
    Location:
    5p13.2
    Exon count:
    46
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (35617863..35814611)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (35864856..36063018)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (35617965..35814713)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr5:35089574-35090075 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:35117544-35118743 Neighboring gene prolactin receptor Neighboring gene Sharpr-MPRA regulatory region 5567 Neighboring gene MPRA-validated peak5224 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:35332547-35333118 Neighboring gene Sharpr-MPRA regulatory region 11164 Neighboring gene small nucleolar RNA U3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:35618008-35618815 Neighboring gene Sharpr-MPRA regulatory region 7256 Neighboring gene RNA, U7 small nuclear 130 pseudogene Neighboring gene uncharacterized LOC105374724 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:35788726-35789925 Neighboring gene NANOG hESC enhancer GRCh37_chr5:35860795-35861296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22472 Neighboring gene Sharpr-MPRA regulatory region 7574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22474 Neighboring gene interleukin 7 receptor Neighboring gene calcyphosine like

    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
    • 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. Novel SPEF2 variants cause male infertility and likely primary ciliary dyskinesia. Lu W, et al. J Assist Reprod Genet, 2024 Jun. PMID 38568462,
    2. Sperm flagellar 2 (SPEF2) is essential for sperm flagellar assembly in humans. Li DY, et al. Asian J Androl, 2022 Jul-Aug. PMID 34755699, Free PMC Article
    3. Biallelic mutations in Sperm flagellum 2 cause human multiple morphological abnormalities of the sperm flagella (MMAF) phenotype. Sha Y, et al. Clin Genet, 2019 Nov. PMID 31278745
    4. Loss-of-function mutations in SPEF2 cause multiple morphological abnormalities of the sperm flagella (MMAF). Liu W, et al. J Med Genet, 2019 Oct. PMID 31151990
    5. Homozygous mutations in SPEF2 induce multiple morphological abnormalities of the sperm flagella and male infertility. Liu C, et al. J Med Genet, 2020 Jan. PMID 31048344

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel SPEF2 variants cause male infertility and likely primary ciliary dyskinesia.
      Title: Novel SPEF2 variants cause male infertility and likely primary ciliary dyskinesia.
    2. Sperm flagellar 2 (SPEF2) is essential for sperm flagellar assembly in humans.
      Title: Sperm flagellar 2 (SPEF2) is essential for sperm flagellar assembly in humans.
    3. Biallelic mutations in Sperm flagellum 2 cause human multiple morphological abnormalities of the sperm flagella (MMAF) phenotype.
      Title: Biallelic mutations in Sperm flagellum 2 cause human multiple morphological abnormalities of the sperm flagella (MMAF) phenotype.
    4. In individuals with primary ciliary dyskinesia and central pair defects, the CP-associated protein SPEF2 is absent in HYDIN-mutant cells. 41 of 189 individuals had undetectable SPEF2 and were subjected to a genetic analysis, which revealed one novel loss-of-function mutation in SPEF2 and 3 reported and 13 novel HYDIN mutations in 15 individuals. A mutation of SPEF2 is causative for PCD with a CP defect.
      Title: SPEF2- and HYDIN-Mutant Cilia Lack the Central Pair-associated Protein SPEF2, Aiding Primary Ciliary Dyskinesia Diagnostics.
    5. Loss-of-function mutations in the SPEF2 gene can cause the Multiple morphological abnormalities of the sperm flagella (MMAF) phenotype in human.
      Title: Loss-of-function mutations in SPEF2 cause multiple morphological abnormalities of the sperm flagella (MMAF).
    6. SPEF2 is a novel gene for human MMAF (multiple morphological abnormalities of the sperm flagella) across the populations. Functional analyses suggested that the deficiency of SPEF2 in the mutated subjects could alter the localisation of other axonemal proteins.
      Title: Homozygous mutations in SPEF2 induce multiple morphological abnormalities of the sperm flagella and male infertility.
    7. Mutations in SPEF2 are associated with multiple morphological abnormalities of the sperm flagella and primary ciliary dyskinesia.
      Title: Novel mutations in SPEF2 causing different defects between flagella and cilia bridge: the phenotypic link between MMAF and PCD.
    8. 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.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    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

    Associated conditions

    Description Tests
    Spermatogenic failure 43
    MedGen: C5231490 OMIM: 618751 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    EBI GWAS Catalog
    Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data.
    EBI GWAS Catalog

    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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    Markers

    Homology

    Clone Names

    • FLJ23164, FLJ23577, FLJ25395, KIAA1770, MGC102842

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    acts_upstream_of_or_within brain morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within epithelial cilium movement involved in extracellular fluid movement ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within respiratory system development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within skeletal system morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in sperm axoneme assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sperm axoneme assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within sperm axoneme assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in manchette IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in manchette ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in sperm flagellum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in sperm midpiece IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in sperm midpiece ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    sperm flagellar protein 2
    Names
    cancer/testis antigen 122
    testis tissue sperm-binding protein Li 47a

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_024867.4 → NP_079143.3  sperm flagellar protein 2 isoform 1

      See identical proteins and their annotated locations for NP_079143.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB051557, AC025448, AK097547, AL832607, BC016773, BC067761, BC110984, BX648691, DA295300
      Consensus CDS
      CCDS43309.1
      UniProtKB/Swiss-Prot
      Q2TAC9, Q96LL6, Q9C093, Q9H5C7, Q9H5Q7
      UniProtKB/TrEMBL
      A0A140VKD0
      Related
      ENSP00000348314.3, ENST00000356031.8
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:686 → 868
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    2. NM_144722.4 → NP_653323.1  sperm flagellar protein 2 isoform 2

      See identical proteins and their annotated locations for NP_653323.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks more than half of the 3'-most exons and has a 3' end that extends into an intron compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC025448, AK058124, BC016773
      Consensus CDS
      CCDS3910.1
      UniProtKB/Swiss-Prot
      Q9C093
      Related
      ENSP00000282469.6, ENST00000282469.10
      Conserved Domains (1) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      35617863..35814611
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514136.4 → XP_011512438.1  sperm flagellar protein 2 isoform X2

      UniProtKB/TrEMBL
      A0A1B0GWD8
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:686 → 868
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    2. XM_047417767.1 → XP_047273723.1  sperm flagellar protein 2 isoform X11

    3. XM_024446219.2 → XP_024301987.1  sperm flagellar protein 2 isoform X17

      Conserved Domains (2) summary
      pfam06294
      Location:8 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:629 → 811
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    4. XM_011514135.4 → XP_011512437.1  sperm flagellar protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A1B0GWD8
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:686 → 868
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    5. XM_005248376.5 → XP_005248433.1  sperm flagellar protein 2 isoform X9

      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:686 → 868
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    6. XM_011514138.4 → XP_011512440.1  sperm flagellar protein 2 isoform X4

      UniProtKB/TrEMBL
      A0A1B0GWD8
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:686 → 868
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    7. XM_011514139.4 → XP_011512441.1  sperm flagellar protein 2 isoform X5

      UniProtKB/TrEMBL
      A0A1B0GWD8
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:686 → 868
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    8. XM_011514137.4 → XP_011512439.1  sperm flagellar protein 2 isoform X3

      UniProtKB/TrEMBL
      A0A1B0GWD8
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:681 → 863
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    9. XM_005248377.5 → XP_005248434.1  sperm flagellar protein 2 isoform X10

      UniProtKB/Swiss-Prot
      Q9C093
      Related
      ENSP00000412125.2, ENST00000440995.6
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:681 → 863
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    10. XM_011514140.3 → XP_011512442.1  sperm flagellar protein 2 isoform X6

      UniProtKB/TrEMBL
      A0A1B0GWD8
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:629 → 811
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    11. XM_017009880.3 → XP_016865369.1  sperm flagellar protein 2 isoform X7

    12. XM_047417768.1 → XP_047273724.1  sperm flagellar protein 2 isoform X12

    13. XM_047417769.1 → XP_047273725.1  sperm flagellar protein 2 isoform X13

    14. XM_017009882.3 → XP_016865371.1  sperm flagellar protein 2 isoform X14

    15. XM_005248378.5 → XP_005248435.1  sperm flagellar protein 2 isoform X15

      UniProtKB/TrEMBL
      D6REZ4
      Conserved Domains (2) summary
      pfam06294
      Location:6 → 97
      CH_2; CH-like domain in sperm protein
      cl17190
      Location:686 → 868
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    16. XM_047417770.1 → XP_047273726.1  sperm flagellar protein 2 isoform X16

      Related
      ENSP00000421593.1, ENST00000509059.5

    17. XM_047417765.1 → XP_047273721.1  sperm flagellar protein 2 isoform X8

    18. XM_047417766.1 → XP_047273722.1  sperm flagellar protein 2 isoform X8

    RNA

    1. XR_925655.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      35864856..36063018
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353530.1 → XP_054209505.1  sperm flagellar protein 2 isoform X2

    2. XM_054353540.1 → XP_054209515.1  sperm flagellar protein 2 isoform X11

    3. XM_054353546.1 → XP_054209521.1  sperm flagellar protein 2 isoform X17

    4. XM_054353529.1 → XP_054209504.1  sperm flagellar protein 2 isoform X1

    5. XM_054353538.1 → XP_054209513.1  sperm flagellar protein 2 isoform X9

    6. XM_054353532.1 → XP_054209507.1  sperm flagellar protein 2 isoform X4

    7. XM_054353533.1 → XP_054209508.1  sperm flagellar protein 2 isoform X5

    8. XM_054353531.1 → XP_054209506.1  sperm flagellar protein 2 isoform X3

    9. XM_054353539.1 → XP_054209514.1  sperm flagellar protein 2 isoform X10

    10. XM_054353534.1 → XP_054209509.1  sperm flagellar protein 2 isoform X6

    11. XM_054353535.1 → XP_054209510.1  sperm flagellar protein 2 isoform X7

    12. XM_054353541.1 → XP_054209516.1  sperm flagellar protein 2 isoform X12

    13. XM_054353542.1 → XP_054209517.1  sperm flagellar protein 2 isoform X13

    14. XM_054353543.1 → XP_054209518.1  sperm flagellar protein 2 isoform X14

    15. XM_054353544.1 → XP_054209519.1  sperm flagellar protein 2 isoform X15

    16. XM_054353545.1 → XP_054209520.1  sperm flagellar protein 2 isoform X16

    17. XM_054353536.1 → XP_054209511.1  sperm flagellar protein 2 isoform X8

    18. XM_054353537.1 → XP_054209512.1  sperm flagellar protein 2 isoform X8

    RNA

    1. XR_008487174.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9C093.2 GenPept UniProtKB/Swiss-Prot:Q9C093

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