CFAP410 (cilia and flagella associated protein 410)

Gene

• Entrez ID: 755
• Gene name: Cilia and flagella associated protein 410
• Gene symbol: CFAP410
• Synonyms (NCBI Gene): C21orf2, LRRC76, RDMS, SMDAX, YF5/A2
• Chromosome: 21
• Chromosome location: 21q22.3
• Summary: Four alternatively spliced transcript variants encoding four different isoforms have been found for this nuclear gene. All isoforms contain leucine-rich repeats. Three of these isoforms are mitochondrial proteins and one of them lacks the target peptide,

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs140451304	C>G,T	Pathogenic, likely-pathogenic	5 prime UTR variant, non coding transcript variant, missense variant, coding sequence variant
rs141195315	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs555164150	C>G,T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs567435284	C>A,G,T	Likely-pathogenic	5 prime UTR variant, missense variant, coding sequence variant, non coding transcript variant
rs746633371	CGTGGCCTGTGCCCTCTCTCTCTGGGGCCGC>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs748531024	->TGCACGCTGTGCAGCT	Pathogenic, likely-pathogenic	Genic upstream transcript variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant, frameshift variant, upstream transcript variant
rs763623409	A>G	Pathogenic	5 prime UTR variant, missense variant, coding sequence variant, non coding transcript variant
rs778222701	C>T	Pathogenic	Splice donor variant
rs922930539	G>A	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1057518441	C>T	Uncertain-significance, pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, missense variant
rs1114167892	A>G	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1114167893	T>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant, 5 prime UTR variant, non coding transcript variant
rs1131690800	T>A	Pathogenic	Intron variant
rs1131690801	T>C	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, missense variant
rs1457263136	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1602071514	C>G	Pathogenic	Splice acceptor variant
rs1602071524	T>C	Pathogenic	Splice acceptor variant
rs1602079250	C>T	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001750	Component	Photoreceptor outer segment	IDA	27548899
GO:0001750	Component	Photoreceptor outer segment	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 26167768, 26290490, 32296183
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IDA	21834987, 26290490
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IDA	9325172
GO:0005739	Component	Mitochondrion	IEA
GO:0005794	Component	Golgi apparatus	IDA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IDA	21834987
GO:0006974	Process	DNA damage response	IEA
GO:0007010	Process	Cytoskeleton organization	IBA
GO:0007010	Process	Cytoskeleton organization	IMP	21834987
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0008360	Process	Regulation of cell shape	IMP	21834987
GO:0030030	Process	Cell projection organization	IEA
GO:0032391	Component	Photoreceptor connecting cilium	IEA
GO:0032391	Component	Photoreceptor connecting cilium	ISS
GO:0036064	Component	Ciliary basal body	IDA	26167768, 26294103
GO:0036064	Component	Ciliary basal body	IEA
GO:0042995	Component	Cell projection	IEA
GO:0060271	Process	Cilium assembly	IEA
GO:0097733	Component	Photoreceptor cell cilium	IEA

Other IDs

• MIM: 603191
• HGNC: 1260
• e!Ensembl: ENSG00000160226

Protein

• UniProt ID: O43822
• Protein name: Cilia- and flagella-associated protein 410 (C21orf-HUMF09G8.5) (Leucine-rich repeat-containing protein 76) (YF5/A2)
• Protein function: Plays a role in cilia formation and/or maintenance (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization (PubMed:21834987). Involved in DNA damage repair (PubMed:26290490). {ECO:0000250|UniProtKB:Q8C6G1
• PDB: 8AXR
• Tissue specificity: TISSUE SPECIFICITY: Widely expressed (PubMed:26974433, PubMed:9325172). Expressed in the retina (PubMed:26294103).
• Sequence:

  MKLTRKMVLTRAKASELHSVRKLNCWGSRLTDISICQEMPSLEVITLSVNSISTLEPVSR
  CQRLSELYLRRNRIPSLAELFYLKGLPRLRVLWLAENPCCGTSPHRYRMTVLRTLPRLQK
  LDNQAVTEEELSRALSEGEEITAAPEREGTGHGGPKLCCTLSSLSSAAETGRDPLDSEEE
  ATSGAQDERGLKPPSRGQFPSLSARDASSSHRGRNVLTAILLLLRELDAEGLEAVQQTVG
  SRLQALRGEEVQEHAE

• Sequence length: 256

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
Axial spondylometaphyseal dysplasia	Pathogenic; Likely pathogenic	rs762237699, rs2146057228, rs1602093658, rs140451304, rs1114167892, rs1114167893, rs778222701, rs1131690800, rs763623409, rs922930539, rs555164150, rs748531024, rs1602071514	RCV005860272 RCV002238696 RCV003989239 RCV000492059 RCV000492049 RCV000492056 RCV000492054 RCV000492061 RCV000492051 RCV000492055 RCV000492060 RCV005632431 RCV002236069	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CFAP410-related disorder	Likely pathogenic; Pathogenic	rs140451304, rs748531024	RCV003409679 RCV004752924	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone dystrophy	Likely pathogenic; Pathogenic	rs140451304	RCV000504995	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Leber congenital amaurosis	Pathogenic	rs1602071524	RCV001002898	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Likely pathogenic; Pathogenic	rs756970705, rs752137434, rs140451304, rs555164150, rs748531024, rs752395624	RCV004815694 RCV004816829 RCV001075775 RCV001073670 RCV000505076 RCV001074619 RCV001074149	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinal dystrophy with or without macular staphyloma	Likely pathogenic; Pathogenic	rs756970705, rs752137434, rs2047687010, rs1568986041, rs2518051350, rs770130993, rs1568992782, rs140451304, rs746633371, rs763623409, rs922930539, rs1131690801, rs748531024, rs1457263136, rs774614339	RCV003225980 RCV003483869 RCV004011296 RCV003389578 RCV003492882 RCV003492885 RCV004584577 RCV001376208 RCV000492057 RCV003227769 RCV003227770 RCV000492052 RCV005632431 RCV003483679 RCV003483780	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinitis pigmentosa	Likely pathogenic; Pathogenic	rs140451304, rs748531024, rs1602071514	RCV000504803 RCV000504882 RCV001002897	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Amyotrophic lateral sclerosis	Uncertain significance	ClinVar CTD, ClinGen, Disgenet, GWAS catalog, Orphanet CTD, ClinGen, Disgenet, GWAS catalog, Orphanet CTD, ClinGen, Disgenet, GWAS catalog, Orphanet CTD, ClinGen, Disgenet, GWAS catalog, Orphanet CTD, ClinGen, Disgenet, GWAS catalog, Orphanet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
ATRIAL FIBRILLATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONE ROD DYSTROPHY	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONE ROD DYSTROPHY-SHORT STATURE SYNDROME	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONE-ROD DYSTROPHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cone-rod dystrophy	Uncertain significance	ClinVar GWAS catalog	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPONDYLOMETAPHYSEAL DYSPLASIA, AXIAL	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ 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 carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	ORPHANET_DG	26974433		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	27455348, 29343210		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	GWASCAT_DG	27455348, 29566793		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	CTD_human_DG	27455348		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Amyotrophic Lateral Sclerosis	Amyotrophic lateral sclerosis	Pubtator	27455348	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Amyotrophic lateral sclerosis	Amyotrophic Lateral Sclerosis	Orphanet			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Amyotrophic Lateral Sclerosis With Dementia	Amyotrophic Lateral Sclerosis With Dementia	CTD_human_DG	27455348		★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis, Guam Form	Amyotrophic lateral sclerosis	CTD_human_DG	27455348		★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Asthenozoospermia	Asthenozoospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	BEFREE	26167768, 26294103		★☆☆☆☆ Found in Text Mining only
Cone Dystrophy	Cone Dystrophy	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone rod dystrophy	Cone-rod dystrophy	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cone-Rod Dystrophies	Cone-rod dystrophy	BEFREE	27548899		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cone-Rod Dystrophy 2	Cone-rod dystrophy	ORPHANET_DG	23105016		★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophy 2	Cone-rod dystrophy	BEFREE	27548899		★☆☆☆☆ Found in Text Mining only
Depressive disorder	Mental Depression	HPO_DG			★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down Syndrome	BEFREE	12624744		★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down Syndrome	LHGDN	15068244		★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down syndrome	Pubtator	26290490	Associate	★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	26294103		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Embryonal nuclear cataract (disorder)	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Jeune syndrome	Jeune syndrome	Pubtator	26974433	Associate	★☆☆☆☆ Found in Text Mining only
Jeune thoracic dystrophy	Jeune Thoracic Dystrophy	GENOMICS_ENGLAND_DG	23105016, 26167768		★☆☆☆☆ Found in Text Mining only
Jeune thoracic dystrophy	Jeune Thoracic Dystrophy	BEFREE	26974433, 28422394		★☆☆☆☆ Found in Text Mining only
Laryngospasm	Laryngospasm	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mood swings	Mood swings	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Nonsyndromic Deafness	BEFREE	9465297		★☆☆☆☆ Found in Text Mining only
Nuclear cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nuclear non-senile cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	26294103		★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polyglandular Type I Autoimmune Syndrome	Polyglandular autoimmune syndrome	BEFREE	9465297		★☆☆☆☆ Found in Text Mining only
Pyle metaphyseal dysplasia	Pyle Metaphyseal Dysplasia	BEFREE	26974433		★☆☆☆☆ Found in Text Mining only
Respiratory Failure	Respiratory Failure	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Degeneration	Retinal degeneration	Pubtator	26974433	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	BEFREE	26294103		★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
RETINAL DYSTROPHY WITH OR WITHOUT MACULAR STAPHYLOMA	Retinal Dystrophy With Or Without Macular Staphyloma	GENOMICS_ENGLAND_DG	23105016, 26167768, 27548899		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
RETINAL DYSTROPHY WITH OR WITHOUT MACULAR STAPHYLOMA	Retinal Dystrophy With Or Without Macular Staphyloma	UNIPROT_DG	26294103, 27548899		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	27548899		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rhizomelia	Rhizomelia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Rod-Cone Dystrophy	Rod-cone dystrophy	BEFREE	27548899		★☆☆☆☆ Found in Text Mining only
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sjogren's Syndrome	Sjogren syndrome	Pubtator	39331939	Stimulate	★☆☆☆☆ Found in Text Mining only
Spondylometaphyseal dysplasia axial	Spondylometaphyseal dysplasia	Pubtator	26974433	Associate	★☆☆☆☆ Found in Text Mining only
Spondylometaphyseal dysplasia, axial	Spondylometaphyseal dysplasia	GENOMICS_ENGLAND_DG	23105016, 26167768, 26974433		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spondylometaphyseal dysplasia, axial	Spondylometaphyseal dysplasia	UNIPROT_DG	26167768, 26974433, 27548899, 28422394		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spondylometaphyseal dysplasia, axial	Spondylometaphyseal dysplasia	BEFREE	26974433, 28123176, 28422394		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spondylometaphyseal dysplasia, axial	Spondylometaphyseal dysplasia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Strudwick syndrome	Strudwick Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Thoracic hypoplasia	Thoracic hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only