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SPEF2 sperm flagellar 2 [ Homo sapiens (human) ]

Gene ID: 79925, updated on 3-Apr-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, Apr 2022]
Expression
Broad expression in endometrium (RPKM 2.4), testis (RPKM 2.1) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
5p13.2
Exon count:
46
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (35617863..35814611)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (35864856..36063018)
105.20220307 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. 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
  2. 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
  3. 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
  4. 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
  5. Novel mutations in SPEF2 causing different defects between flagella and cilia bridge: the phenotypic link between MMAF and PCD. Tu C, et al. Hum Genet, 2020 Feb. PMID 31942643

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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).
  5. 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.
  6. 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.
  7. 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.
  8. 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)

Genotypes

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

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
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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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_2023_10

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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