SPEF2 sperm flagellar 2 [Homo sapiens (human)] - Gene

Summary

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

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_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Novel SPEF2 variants cause male infertility and likely primary ciliary dyskinesia.
Title: Novel SPEF2 variants cause male infertility and likely primary ciliary dyskinesia.
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.
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.
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.
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).
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.

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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 EBI GWAS CatalogPubMed
Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data. 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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Markers

SGC38369 (e-PCR)
- UniSTS:23569

RH118857 (e-PCR)
- UniSTS:138839

D5S395 (e-PCR), detects polymorphism
- UniSTS:47454

D5S395 (e-PCR), detects polymorphism
- UniSTS:25211

SHGC-154301 (e-PCR)
- UniSTS:178063

G65480 (e-PCR)
- UniSTS:166592

D5S395 (e-PCR), detects polymorphism
- UniSTS:181719

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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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_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 ...
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

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

35617863..35814611

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
XM_047417767.1 → XP_047273723.1 sperm flagellar protein 2 isoform X11
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
XM_017009880.3 → XP_016865369.1 sperm flagellar protein 2 isoform X7
XM_047417768.1 → XP_047273724.1 sperm flagellar protein 2 isoform X12
XM_047417769.1 → XP_047273725.1 sperm flagellar protein 2 isoform X13
XM_017009882.3 → XP_016865371.1 sperm flagellar protein 2 isoform X14
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 ...
XM_047417770.1 → XP_047273726.1 sperm flagellar protein 2 isoform X16

Related

ENSP00000421593.1, ENST00000509059.5
XM_047417765.1 → XP_047273721.1 sperm flagellar protein 2 isoform X8
XM_047417766.1 → XP_047273722.1 sperm flagellar protein 2 isoform X8