SPEF2 (sperm flagellar 2)

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Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 79925
• Gene name: Sperm flagellar 2
• Gene symbol: SPEF2
• Synonyms (NCBI Gene): CT122, KPL2, SPGF43
• Chromosome: 5
• Chromosome location: 5p13.2

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1391102782	C>-	Pathogenic	Frameshift variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant

miRNA Show/Hide all (13)

miRTarBase ID	miRNA	Experiments	Reference
MIRT1383679	hsa-miR-4255	CLIP-seq
MIRT1383680	hsa-miR-4276	CLIP-seq
MIRT1383681	hsa-miR-4325	CLIP-seq
MIRT1383682	hsa-miR-450b-5p	CLIP-seq
MIRT1383683	hsa-miR-507	CLIP-seq
MIRT1383684	hsa-miR-557	CLIP-seq
MIRT2114832	hsa-miR-4445	CLIP-seq
MIRT2114833	hsa-miR-4477b	CLIP-seq
MIRT2114834	hsa-miR-500a	CLIP-seq
MIRT2114835	hsa-miR-554	CLIP-seq
MIRT2114836	hsa-miR-587	CLIP-seq
MIRT2114837	hsa-miR-885-5p	CLIP-seq
MIRT2631103	hsa-miR-548c-3p	CLIP-seq

Gene ontology (GO) Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002177	Component	Manchette	IBA
GO:0002177	Component	Manchette	ISS
GO:0003351	Process	Epithelial cilium movement involved in extracellular fluid movement	ISS
GO:0005576	Component	Extracellular region	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0005794	Component	Golgi apparatus	IEA
GO:0005794	Component	Golgi apparatus	ISS
GO:0005829	Component	Cytosol	IDA
GO:0005929	Component	Cilium	IDA
GO:0005929	Component	Cilium	IEA
GO:0007283	Process	Spermatogenesis	IEA
GO:0007283	Process	Spermatogenesis	ISS
GO:0007288	Process	Sperm axoneme assembly	IBA
GO:0007288	Process	Sperm axoneme assembly	IMP	31048344, 31151990
GO:0007288	Process	Sperm axoneme assembly	ISS
GO:0016604	Component	Nuclear body	IDA
GO:0030154	Process	Cell differentiation	IEA
GO:0031514	Component	Motile cilium	IEA
GO:0036126	Component	Sperm flagellum	IDA	31048344, 31151990, 31278745
GO:0042995	Component	Cell projection	IEA
GO:0048705	Process	Skeletal system morphogenesis	ISS
GO:0048854	Process	Brain morphogenesis	ISS
GO:0060541	Process	Respiratory system development	ISS
GO:0097225	Component	Sperm midpiece	IBA
GO:0097225	Component	Sperm midpiece	ISS

Other IDs

• MIM: 610172
• HGNC: 26293
• e!Ensembl: ENSG00000152582

Protein

• UniProt ID: Q9C093
• Protein name: Sperm flagellar protein 2 (Protein KPL2)
• Protein function: Required for correct axoneme development in spermatozoa. Important for normal development of the manchette and sperm head morphology. Essential for male fertility. Plays a role in localization of the intraflagellar transport protein IFT20 to the
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00406	ADK	671 → 764		Domain
  PF06294	CH_2	5 → 102	CH-like domain in sperm protein	Domain

• Sequence:

  MSEILCQWLNKELKVSRTVSPKSFAKAFSSGYLLGEVLHKFELQDDFSEFLDSRVSSAKL
  NNFSRLEPTLNLLGVQFDQNVAHGIITEKPGVATKLLYQLYIALQKKKKSGLTGVEMQTM
  QRLTNLRLQNMKSDTFQERLRHMIPRQTDFNLMRITYRFQEKYKHVKEDLAHLHFEKLER
  FQKLKEEQRCFDIEKQYLNRRRQNEIMAKIQAAIIQIPKPASNRTLKALEAQKMMKKKKE
  AEDVADEIKKFEALIKKDLQAKESASKTSLDTAGQTTTDLLNTYSDDEYIKKIQKRLEED
  AFAREQREKRRRKLLMDQLIAHEAQEEAYREEQLINRLMRQSQQERRIAVQLMHVRHEKE
  VLWQNRIFREKQHEERRLKDFQDALDREAALAKQAKIDFEEQFLKEKRFHDQIAVERAQA
  RYEKHYSVCAEILDQIVDLSTKVADYRMLTNNLIPYKLMHDWKELFFNAKPIYEQASVKT
  LPANPSREQLTELEKRDLLDTNDYEEYKNMVGEWALPEEMVDNLPPSNNCILGHILHRLA
  EKSLPPRAESTTPELPSFAVKGCLLGKTLSGKTTILRSLQKDFPIQILSIDTLVQEAIQA
  FHDNEKVSEVLPIQKNDEEDALPVLQEEIKESQDPQHVFSAGPVSDEVLPETEGETMLSA
  NADKTPKAEEVKSSDSFLKLTTRAQLGAKSEQLLKKGKSIPDVLLVDIIVNAINEIPVNQ
  DCILDGFPMTLNQAQLLEEALTGCNRNLTEVERKKAQKSTLAIDPATSKEIPLPSPAFDF
  VILLDVSDTSSMSRMNDIIAEELSYKTAHEDISQRVAAENQDKDGDQNLRDQIQHRIIGF
  LDNWPLLEQWFSEPENILIKINAEIDKESLCEKVKEILTTEIAKKKNKVEKKLEEKEAEK
  KAAASLAELPLPTPPPAPPPEPEKEKEIHQSHVASKTPTAKGKPQSEAPHGKQESLQEGK
  GKKGETALKRKGSPKGKSSGGKVPVKKSPADSTDTSPVAIVPQPPKPGSEEWVYVNEPVP
  EEMPLFLVPYWELIENSYINTIKTVLRHLREDQHTVLAYLYEIRTSFQEFLKRPDHKQDF
  VAQWQADFNSLPDDLWDDEETKAELHQRVNDLRDRLWDICDARKEEAEQERLDIINESWL
  QDTLGMTMNHFFSLMQAELNRFQDTKRLLQDYYWGMESKIPVEDNKRFTRIPLVQLDSKD
  NSESQLRIPLVPRISISLETVTPKPKTKSVLKGKMDNSLENVESNFEADEKLVMDTWQQA
  SLAVSHMVAAEIHQRLMEEEKENQPADPKEKSPQMGANKKVKKEPPKKKQEDKKPKGKSP
  PMAEATPVIVTTEEIAEIKRKNELRVKIKEEHLAALQFEEIATQFRLELIKTKALALLED
  LVTKVVDVYKLMEKWLGERYLNEMASTEKLTDVARYHIETSTKIQNELYLSQEDFFINGN
  IKVFPDPPPSIRPPPVEKEEDGTLTIEQLDSLRDQFLDMAPKGIIGNKAFTDILIDLVTL
  NLGTNNFPSNWMHLTQPELQELTSLLTVNSEFVDWRKFLLVTSMPWPIPLEEELLETLQK
  FKAVDKEQLGTITFEQYMQAGLWFTGDEDIKIPENPLEPLPFNRQEHLIEFFFRLFADYE
  KDPPQLDYTQMLLYFACHPDTVEGVYRALSVAVGTHVFQQVKASIPSAEKTSSTDAGPAE
  EFPEPEENAAREERKLKDDTEKREQKDEEIPENANNEKMSMETLLKVFKGGSEAQDSNRF
  ASHLKIENIYAEGFIKTFQDLGAKNLEPIEVAVLLKHPFIQDLISNYSDYKFPDIKIILQ
  RSEHVQGSDGERSPSRHTEEKK

• Sequence length: 1822

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Primary ciliary dyskinesia	Pathogenic	rs1739374011	RCV001089640	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SPEF2-related disorder	Likely pathogenic	rs1239348737, rs1754689321	RCV003397824 RCV003903964	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spermatogenic failure 43	Pathogenic	rs1391102782, rs1375975527, rs1230916222, rs1580704451, rs1580383744, rs1580783651, rs1580529760	RCV000993859 RCV000993860 RCV000993861 RCV000993862 RCV000993863 RCV000993864 RCV000993865	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (38)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTHMA	—	GWAS catalog	31619474, 32296059, 34594039, 36344522, 36777996, 41213931	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATOPIC ASTHMA	—	GWAS catalog	31669095	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATOPIC ECZEMA	—	GWAS catalog	40164604	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATROPHIC MACULAR DEGENERATION	—	GWAS catalog	26691988	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOIMMUNE THYROID DISEASE	—	GWAS catalog	32581359, 37002690	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BILIARY LIVER CIRRHOSIS	—	GWAS catalog	23000144, 30643196, 34033851	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CILIARY MOTILITY DISORDERS	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL IMPAIRMENT OF SPERMATOZOA MOTILITY	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DUCHENNE MUSCULAR DYSTROPHY	—	GWAS catalog	30014611	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOTHYROIDISM	—	GWAS catalog	30595370, 34594039, 39067062, 41238958	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Uncertain significance	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	21244703	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NASAL CAVITY POLYP	—	GWAS catalog	36653354	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NASAL DISORDER	—	GWAS catalog	36653354	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY BILIARY CIRRHOSIS	—	GWAS catalog	23000144, 30643196, 34033851	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	39885523, 40021644	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Uncertain significance	ClinVar Disgenet	—	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SEASONAL ALLERGIC RHINITIS	—	GWAS catalog	31361310, 39789286	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WET MACULAR DEGENERATION	—	GWAS catalog	26691988	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (21)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Asthenozoospermia	Asthenozoospermia	Pubtator	34755699	Associate	★☆☆☆☆ Found in Text Mining only
Ciliary Dyskinesia, Primary, 1, With Or Without Situs Inversus	Ciliary Dyskinesia	ORPHANET_DG	31545650		★☆☆☆☆ Found in Text Mining only
Ciliary Motility Disorders	Ciliary dyskinesia	Pubtator	38568462	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hydrocephalus	Hydrocephalus	BEFREE	29339787, 30190587		★☆☆☆☆ Found in Text Mining only
Infertility	Infertility	Pubtator	38568462	Associate	★☆☆☆☆ Found in Text Mining only
Infertility Male	Male infertility	Pubtator	38568462	Associate	★☆☆☆☆ Found in Text Mining only
Kartagener Syndrome	Kartagener Syndrome	BEFREE	29339787		★☆☆☆☆ Found in Text Mining only
Kartagener Syndrome	Kartagener Syndrome	ORPHANET_DG	31545650		★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	Pubtator	37801226	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Macular Degeneration	Macular degeneration	Pubtator	32246154	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	GWASCAT_DG	21244703		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Sclerosis	Multiple Sclerosis	GWASDB_DG	21244703		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	31770211	Associate	★☆☆☆☆ Found in Text Mining only
Non-syndromic male infertility due to sperm motility disorder	Non-Syndromic Male Infertility Due To Sperm Motility Disorder	Orphanet			★☆☆☆☆ Found in Text Mining only
Pancreatitis	Pancreatitis	Pubtator	28574850	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatitis	Pancreatitis	BEFREE	28574850		★☆☆☆☆ Found in Text Mining only
Polynesian Bronchiectasis	Kartagener syndrome	ORPHANET_DG	31545650		★☆☆☆☆ Found in Text Mining only
Primary Ciliary Dyskinesia	Ciliary dyskinesia	BEFREE	29339787, 31545650		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Primary Ciliary Dyskinesia	Ciliary dyskinesia	ORPHANET_DG	31545650		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Primary ciliary dyskinesia	Ciliary dyskinesia	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thrombosis	Thrombosis	Pubtator	28574850	Associate	★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

AK7 3 shared diseasesCiliary dyskinesia, Congenital impairment of spermatozoa motility, Spermatogenic failure 7 shared evidence sourcesDisgenet (Ciliary dyskinesia), ClinGen (Ciliary dyskinesia), GenCC (Ciliary dyskinesia), Disgenet (Congenital impairment of spermatozoa motility), Disgenet (Spermatogenic failure), HPO (Spermatogenic failure), ClinVar (Spermatogenic failure) Related via 3 shared diseases including Ciliary dyskinesia, Congenital impairment of spermatozoa motility — evidence mostly Disgenet. DNAH1 4 shared diseasesCiliary dyskinesia, Congenital impairment of spermatozoa motility, Spermatogenic failure, primary ciliary dyskinesia 8 shared evidence sourcesDisgenet (Ciliary dyskinesia), ClinGen (Ciliary dyskinesia), Disgenet (Congenital impairment of spermatozoa motility), Orphanet (Ciliary dyskinesia), Disgenet (Spermatogenic failure), HPO (Spermatogenic failure), ClinVar (Spermatogenic failure), ClinGen (primary ciliary dyskinesia) Related via 4 shared diseases including Ciliary dyskinesia, Congenital impairment of spermatozoa motility — evidence mostly Disgenet. CFAP43 4 shared diseasesCiliary dyskinesia, Congenital impairment of spermatozoa motility, Spermatogenic failure, primary ciliary dyskinesia 8 shared evidence sourcesDisgenet (Ciliary dyskinesia), ClinGen (Ciliary dyskinesia), Disgenet (Congenital impairment of spermatozoa motility), Disgenet (Spermatogenic failure), HPO (Spermatogenic failure), CTD (Spermatogenic failure), ClinVar (Spermatogenic failure), ClinGen (primary ciliary dyskinesia) Related via 4 shared diseases including Ciliary dyskinesia, Congenital impairment of spermatozoa motility — evidence mostly Disgenet. CFAP57 3 shared diseasesCiliary dyskinesia, Spermatogenic failure, primary ciliary dyskinesia 5 shared evidence sourcesDisgenet (Ciliary dyskinesia), ClinGen (Ciliary dyskinesia), HPO (Spermatogenic failure), ClinVar (Spermatogenic failure), ClinGen (primary ciliary dyskinesia) Related via 3 shared diseases including Ciliary dyskinesia, Spermatogenic failure — evidence mostly ClinGen. DAW1 3 shared diseasesCiliary dyskinesia, Seasonal allergic rhinitis, primary ciliary dyskinesia 6 shared evidence sourcesDisgenet (Ciliary dyskinesia), ClinGen (Ciliary dyskinesia), GenCC (Ciliary dyskinesia), Orphanet (Ciliary dyskinesia), GWAS catalog (Seasonal allergic rhinitis), ClinGen (primary ciliary dyskinesia) Related via 3 shared diseases including Ciliary dyskinesia, Seasonal allergic rhinitis — evidence mostly ClinGen.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
AK7	3	["Ciliary dyskinesia","Congenital impairment of spermatozoa motility","Spermatogenic failure"]	0	[]	7	["Disgenet (Ciliary dyskinesia)","ClinGen (Ciliary dyskinesia)","GenCC (Ciliary dyskinesia)","Disgenet (Congenital impairment of spermatozoa motility)","Disgenet (Spermatogenic failure)","HPO (Spermatogenic failure)","ClinVar (Spermatogenic failure)"]
DNAH1	4	["Ciliary dyskinesia","Congenital impairment of spermatozoa motility","Spermatogenic failure","primary ciliary dyskinesia"]	0	[]	8	["Disgenet (Ciliary dyskinesia)","ClinGen (Ciliary dyskinesia)","Disgenet (Congenital impairment of spermatozoa motility)","Orphanet (Ciliary dyskinesia)","Disgenet (Spermatogenic failure)","HPO (Spermatogenic failure)","ClinVar (Spermatogenic failure)","ClinGen (primary ciliary dyskinesia)"]
CFAP43	4	["Ciliary dyskinesia","Congenital impairment of spermatozoa motility","Spermatogenic failure","primary ciliary dyskinesia"]	0	[]	8	["Disgenet (Ciliary dyskinesia)","ClinGen (Ciliary dyskinesia)","Disgenet (Congenital impairment of spermatozoa motility)","Disgenet (Spermatogenic failure)","HPO (Spermatogenic failure)","CTD (Spermatogenic failure)","ClinVar (Spermatogenic failure)","ClinGen (primary ciliary dyskinesia)"]
CFAP57	3	["Ciliary dyskinesia","Spermatogenic failure","primary ciliary dyskinesia"]	0	[]	5	["Disgenet (Ciliary dyskinesia)","ClinGen (Ciliary dyskinesia)","HPO (Spermatogenic failure)","ClinVar (Spermatogenic failure)","ClinGen (primary ciliary dyskinesia)"]
DAW1	3	["Ciliary dyskinesia","Seasonal allergic rhinitis","primary ciliary dyskinesia"]	0	[]	6	["Disgenet (Ciliary dyskinesia)","ClinGen (Ciliary dyskinesia)","GenCC (Ciliary dyskinesia)","Orphanet (Ciliary dyskinesia)","GWAS catalog (Seasonal allergic rhinitis)","ClinGen (primary ciliary dyskinesia)"]

Diseases Linked via Similar Genes

Teratozoospermia Linked via 2 of 5 related genesDNAH1, CFAP43 Diabetes mellitus type 2 Linked via 2 of 5 related genesDNAH1, CFAP57 Gout Linked via 1 of 5 related genesDNAH1 Hypertrophic cardiomyopathy Linked via 1 of 5 related genesDNAH1 Tumor predisposition syndrome Linked via 1 of 5 related genesDNAH1

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Teratozoospermia	2	["DNAH1","CFAP43"]
Diabetes mellitus type 2	2	["DNAH1","CFAP57"]
Gout	1	["DNAH1"]
Hypertrophic cardiomyopathy	1	["DNAH1"]
Tumor predisposition syndrome	1	["DNAH1"]