CFAP410

cilia and flagella associated protein 410

Basic information

Region (hg38): 21:44328943-44339402

Previous symbols: [ "C21orf2" ]

Links

ENSG00000160226 ∙ NCBI:755 ∙ OMIM:603191 ∙ HGNC:1260 ∙ Uniprot:O43822 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyotrophic lateral sclerosis (Supportive), mode of inheritance: AD
• cone-rod dystrophy (Supportive), mode of inheritance: AD
• axial spondylometaphyseal dysplasia (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinal dystrophy with or without macular staphyloma; Spondylometaphyseal dysplasia, axial	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Ophthalmologic	23105016; 26167768; 26294103;26974433; 26992781; 27548899

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP410 gene.

• not provided (340 variants)
• Retinal dystrophy with or without macular staphyloma (18 variants)
• Retinal dystrophy (9 variants)
• CFAP410-related condition (8 variants)
• not specified (7 variants)
• Axial spondylometaphyseal dysplasia (7 variants)
• Retinitis pigmentosa (4 variants)
• Cone-rod dystrophy (2 variants)
• Amyotrophic lateral sclerosis (1 variants)
• Cone dystrophy (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP410 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	69	6	77
missense	2	3	142	9	8	164
nonsense	3					3
start loss			1		1	2
frameshift	9	4	6			19
inframe indel		1	7	1		9
splice donor/acceptor (+/-2bp)	4	2	2			8
splice region			6	13	1	20
non coding	1	1		26	19	47
Total	19	11	160	105	34

Highest pathogenic variant AF is 0.0000790

Variants in CFAP410

This is a list of pathogenic ClinVar variants found in the CFAP410 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
21-44330063-C-T			Benign (May 11, 2021)
21-44330165-C-T			Benign (May 11, 2021)
21-44330168-G-A			Benign (May 10, 2021)
21-44330194-G-A		CFAP410-related disorder	Likely benign (May 28, 2019)
21-44330203-C-T			Uncertain significance (Nov 01, 2022)
21-44330204-G-A			Likely benign (Jun 25, 2023)
21-44330206-C-T		CFAP410-related disorder	Conflicting classifications of pathogenicity (Jan 31, 2024)
21-44330207-G-A			Likely benign (Apr 15, 2023)
21-44330208-T-C			Uncertain significance (Jun 24, 2022)
21-44330217-A-C			Uncertain significance (Aug 21, 2022)
21-44330219-C-T			Likely benign (Nov 27, 2023)
21-44330222-T-C			Likely benign (Jul 04, 2022)
21-44330225-C-T			Likely benign (Jun 23, 2020)
21-44330229-C-A			Uncertain significance (Mar 23, 2023)
21-44330229-C-T			Benign (Jan 26, 2024)
21-44330230-G-A			Uncertain significance (Sep 19, 2022)
21-44330238-T-TGCAGCCGGCTGCCC			Uncertain significance (Jul 26, 2022)
21-44330240-C-T		CFAP410-related disorder	Likely benign (Aug 14, 2023)
21-44330244-C-T			Uncertain significance (Feb 08, 2022)
21-44330245-G-A			Uncertain significance (Jul 26, 2022)
21-44330246-G-GCTGCCCACAGTCTGCTGCACGGCCTCCAGCCCCT			Uncertain significance (Aug 23, 2022)
21-44330249-G-GC			Uncertain significance (Jun 15, 2022)
21-44330252-C-A			Likely benign (Mar 09, 2022)
21-44330255-A-C			Likely benign (Jul 26, 2018)
21-44330256-G-A			Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP410	protein_coding	protein_coding	ENST00000397956	7	10459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.29e-7	0.341	125717	0	26	125743	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.165	244	237	1.03	0.0000165	2320
Missense in Polyphen		72	66.759	1.0785		709
Synonymous	-0.534	117	110	1.06	0.00000764	831
Loss of Function	0.518	11	13.0	0.845	6.44e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.0000483	0.0000462
European (Non-Finnish)	0.000154	0.000123
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000987	0.0000980
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Function: 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, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:26290490}.
• Disease: DISEASE: Spondylometaphyseal dysplasia, axial (SMDAX) [MIM:602271]: A form of spondylometaphyseal dysplasia, a group of short stature disorders distinguished by abnormalities in the vertebrae and the metaphyses of the tubular bones. SMDAX is characterized by metaphyseal changes of truncal-juxtatruncal bones, including the proximal femora. Main clinical features are postnatal growth failure, rhizomelic short stature in early childhood evolving into short trunk in late childhood, and thoracic hypoplasia that may cause mild to moderate respiratory problems in the neonatal period and later susceptibility to airway infection. Impaired visual acuity comes to medical attention in early life and function rapidly deteriorates. Retinal changes are diagnosed as retinitis pigmentosa or pigmentary retinal degeneration on fundoscopic examination and cone-rod dystrophy on electroretinogram. The radiological hallmarks include short ribs with flared, cupped anterior ends, mild spondylar dysplasia, lacy iliac crests, and metaphyseal irregularities essentially confined to the proximal femora. {ECO:0000269|PubMed:26167768, ECO:0000269|PubMed:26974433, ECO:0000269|PubMed:27548899, ECO:0000269|PubMed:28422394}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.89

Haploinsufficiency Scores

• pHI: 0.0737
• hipred: N
• hipred_score: 0.146
• ghis: 0.417

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: 1810043G02Rik

Gene ontology

• Biological process: cytoskeleton organization;regulation of cell shape;DNA damage response, detection of DNA damage;motile cilium assembly;cilium assembly;cilium movement involved in cell motility
• Cellular component: photoreceptor outer segment;cytoplasm;mitochondrion;plasma membrane;cilium;motile cilium;photoreceptor connecting cilium;ciliary basal body
• Molecular function: molecular_function;protein binding