CFAP45

cilia and flagella associated protein 45, the group of Cilia and flagella associated

Basic information

Region (hg38): 1:159872364-159900165

Previous symbols: [ "CCDC19" ]

Links

ENSG00000213085 ∙ NCBI:25790 ∙ OMIM:605152 ∙ HGNC:17229 ∙ Uniprot:Q9UL16 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Heterotaxy, visceral, 11, autosomal, with male infertility	AR	Cardiovascular; Pulmonary	The condition can involve congenital cardiac anomalies, and awareness may allow early management; Though pulmonary manifestations have been described as relatively mild, awareness may allow management of respiratory sequelae	Cardiovascular; Gastrointestinal; Genitourinary; Pulmonary	33139725

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP45 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP45 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				3		3
missense			59	2	1	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	60	5	1

Variants in CFAP45

This is a list of pathogenic ClinVar variants found in the CFAP45 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-159872513-T-C		not specified	Uncertain significance (Dec 09, 2024)
1-159872523-G-A		not specified	Uncertain significance (Jun 30, 2022)
1-159872966-T-A		not specified	Uncertain significance (Feb 14, 2024)
1-159872969-T-C		not specified	Uncertain significance (Aug 15, 2023)
1-159872978-C-T		not specified	Uncertain significance (Jun 10, 2024)
1-159872983-C-A		not specified	Uncertain significance (May 04, 2022)
1-159872983-C-T		not specified	Uncertain significance (Sep 14, 2021)
1-159872984-G-A		not specified	Uncertain significance (Apr 21, 2022)
1-159872997-C-G		not specified	Uncertain significance (Feb 14, 2023)
1-159873000-G-A			Likely benign (Feb 01, 2023)
1-159873019-C-T		not specified	Uncertain significance (Jan 18, 2025)
1-159873025-T-C		not specified	Uncertain significance (Feb 16, 2023)
1-159873044-G-C		not specified	Uncertain significance (Jan 06, 2023)
1-159873044-GGTTCT-A		Heterotaxy, visceral, 11, autosomal, with male infertility	Pathogenic (Nov 05, 2021)
1-159873074-G-T		not specified	Uncertain significance (Apr 24, 2023)
1-159873082-C-G		not specified	Uncertain significance (Aug 04, 2023)
1-159873083-G-A		not specified	Uncertain significance (Jul 21, 2021)
1-159873086-G-A		not specified	Uncertain significance (May 17, 2023)
1-159873100-T-A		not specified	Uncertain significance (Apr 23, 2024)
1-159873109-C-T		not specified	Uncertain significance (Feb 07, 2023)
1-159873140-G-A		not specified	Uncertain significance (Jun 12, 2023)
1-159873163-T-C		not specified	Uncertain significance (May 17, 2023)
1-159876582-G-A			Likely benign (Jan 01, 2024)
1-159876587-G-A		not specified	Uncertain significance (Jan 28, 2025)
1-159876626-C-A		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP45	protein_coding	protein_coding	ENST00000368099	12	27800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.54e-14	0.554	125638	0	110	125748	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.546	356	328	1.08	0.0000216	3655
Missense in Polyphen		118	104.2	1.1324		1113
Synonymous	1.18	98	114	0.859	0.00000610	988
Loss of Function	1.57	26	36.2	0.719	0.00000225	368

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00106
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000388	0.000387
Middle Eastern	0.000544	0.000544
South Asian	0.000392	0.000392
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.120

Intolerance Scores

• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.66

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.282
• ghis: 0.418

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap45

Gene ontology

• Cellular component: nucleus;nucleoplasm;cilium