CFAP418

cilia and flagella associated protein 418

Basic information

Region (hg38): 8:95244912-95269201

Previous symbols: [ "C8orf37" ]

Links

ENSG00000156172 ∙ NCBI:157657 ∙ OMIM:614477 ∙ HGNC:27232 ∙ Uniprot:Q96NL8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cone-rod dystrophy 16 (Definitive), mode of inheritance: AR
• cone-rod dystrophy 16 (Moderate), mode of inheritance: AR
• bardet-biedl syndrome 21 (Limited), mode of inheritance: AR
• cone-rod dystrophy 16 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bardet-Biedl syndrome 21	AR	Endocrine	Medical management of obesity with melanocortin-4 receptor (MC4R) agonist (setmelanotide) may be beneficial	Dental; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal	22177090; 26854863; 27008867; 36356613

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP418 gene.

• not provided (146 variants)
• Cone-rod dystrophy 16 (61 variants)
• Retinitis pigmentosa (58 variants)
• Bardet-biedl syndrome 21;Retinitis pigmentosa;Cone-rod dystrophy 16 (12 variants)
• CFAP418-related condition (7 variants)
• not specified (4 variants)
• Bardet-biedl syndrome 21 (4 variants)
• Cone-rod dystrophy 16;Bardet-biedl syndrome 21;Retinitis pigmentosa (3 variants)
• Bardet-biedl syndrome 21;Cone-rod dystrophy 16;Retinitis pigmentosa (3 variants)
• Retinitis pigmentosa;Bardet-biedl syndrome 21;Cone-rod dystrophy 16 (2 variants)
• C8orf37-Related Disorders (2 variants)
• Retinitis pigmentosa 64 (1 variants)
• Retinitis Pigmentosa, Recessive (1 variants)
• Autosomal recessive retinitis pigmentosa (1 variants)
• Cone-Rod Dystrophy, Recessive (1 variants)
• Cone-rod dystrophy 16;Retinitis pigmentosa;Bardet-biedl syndrome 21 (1 variants)
• Retinal dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP418 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	13		15
missense	1		77	3		81
nonsense	1	2				3
start loss			1			1
frameshift	7	2	1			10
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			4	4		8
non coding			31	30	6	67
Total	9	4	113	46	6

Highest pathogenic variant AF is 0.00000658

Variants in CFAP418

This is a list of pathogenic ClinVar variants found in the CFAP418 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-95245000-C-A		Retinitis pigmentosa • Cone-rod dystrophy 16	Uncertain significance (Jan 13, 2018)
8-95245068-G-T		Retinitis pigmentosa • Cone-rod dystrophy 16	Uncertain significance (Jan 13, 2018)
8-95245092-A-G		Cone-rod dystrophy 16 • Retinitis pigmentosa	Benign (Jan 13, 2018)
8-95245119-T-C		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
8-95245125-G-A		Retinitis pigmentosa • Cone-rod dystrophy 16	Uncertain significance (Apr 27, 2017)
8-95245198-A-T		Retinitis pigmentosa • Cone-rod dystrophy 16	Benign/Likely benign (Jan 13, 2018)
8-95245287-G-A		Cone-rod dystrophy 16 • Retinitis pigmentosa	Conflicting classifications of pathogenicity (Jan 13, 2018)
8-95245405-G-A		Cone-rod dystrophy 16 • Retinitis pigmentosa	Conflicting classifications of pathogenicity (Jan 12, 2018)
8-95245405-G-C		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
8-95245451-A-C		Cone-rod dystrophy 16 • Retinitis pigmentosa	Conflicting classifications of pathogenicity (Jan 12, 2018)
8-95245454-A-G		Cone-rod dystrophy 16 • Retinitis pigmentosa	Benign (Jan 12, 2018)
8-95245488-T-C		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
8-95245515-C-T		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
8-95245523-G-A		Retinitis pigmentosa • Cone-rod dystrophy 16	Benign/Likely benign (Apr 27, 2017)
8-95245600-G-C		Retinitis pigmentosa • Cone-rod dystrophy 16	Uncertain significance (Jan 13, 2018)
8-95245608-G-A		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
8-95245668-G-C		Cone-rod dystrophy 16 • Retinitis pigmentosa	Benign/Likely benign (Jan 13, 2018)
8-95245713-C-T		Retinitis pigmentosa • Cone-rod dystrophy 16	Uncertain significance (Jan 12, 2018)
8-95245747-A-T		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
8-95245806-T-C		Retinitis pigmentosa • Cone-rod dystrophy 16	Benign/Likely benign (Jan 12, 2018)
8-95245930-A-T		Retinitis pigmentosa • Cone-rod dystrophy 16	Uncertain significance (Jan 13, 2018)
8-95245942-C-A		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
8-95245950-A-G		Cone-rod dystrophy 16 • Retinitis pigmentosa	Benign/Likely benign (Jan 13, 2018)
8-95245988-A-C		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
8-95245989-T-A		Cone-rod dystrophy 16 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP418	protein_coding	protein_coding	ENST00000286688	6	24283

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000237	0.521	125731	0	11	125742	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0721	117	115	1.02	0.00000562	1371
Missense in Polyphen		41	41.266	0.99355		486
Synonymous	1.49	27	38.8	0.695	0.00000179	361
Loss of Function	0.611	8	10.1	0.793	4.22e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000604	0.0000604
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000548	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in photoreceptor outer segment disk morphogenesis (By similarity). {ECO:0000250|UniProtKB:Q3UJP5}.
• Disease: DISEASE: Retinitis pigmentosa 64 (RP64) [MIM:614500]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:22177090}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bardet-Biedl syndrome 21 (BBS21) [MIM:617406]: A form of Bardet-Biedl syndrome, a syndrome characterized by usually severe pigmentary retinopathy, early-onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:26854863, ECO:0000269|PubMed:27008867}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.448
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.144
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: 2610301B20Rik
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: si:dkey-242e21.4
• Affected structure: Kupffer's vesicle
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: photoreceptor cell morphogenesis
• Cellular component: photoreceptor inner segment;cytoplasm;cytosol;plasma membrane;cell junction;ciliary base
• Molecular function: protein binding