CFAP43

cilia and flagella associated protein 43, the group of WD repeat domain containing|Cilia and flagella associated

Basic information

Region (hg38): 10:104129888-104232364

Previous symbols: [ "C10orf79", "WDR96" ]

Links

ENSG00000197748

∙ NCBI:80217 ∙ OMIM:617558 ∙ HGNC:26684 ∙ Uniprot:Q8NDM7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

spermatogenic failure 19 (Limited), mode of inheritance: AR
normal pressure hydrocephalus (Limited), mode of inheritance: AD
non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR
spermatogenic failure 19 (Definitive), mode of inheritance: AR
primary ciliary dyskinesia (Disputed Evidence), mode of inheritance: Unknown
normal pressure hydrocephalus (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 19	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	Genitourinary	28552195

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP43 gene.

not provided (1 variants)
Normal pressure hydrocephalus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP43 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				19 clinvar	6 clinvar	25
missense			80 clinvar	12 clinvar	6 clinvar	98
nonsense	2 clinvar	1 clinvar				3
start loss						0
frameshift		1 clinvar				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	3	5
non coding						0
Total	2	2	80	31	12

Highest pathogenic variant AF is 0.000171

Variants in CFAP43

This is a list of pathogenic ClinVar variants found in the CFAP43 region.

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

Position	Phenotype	Significance	ClinVar
10-104130185-A-G	not specified	Uncertain significance (Jan 27, 2022)	2274312
10-104130189-C-T	not specified	Uncertain significance (Feb 11, 2022)	2277115
10-104130258-T-A	not specified	Uncertain significance (Feb 28, 2023)	2491181
10-104131391-A-C	not specified	Uncertain significance (Jan 04, 2024)	3143473
10-104131391-A-G	CFAP43-related disorder	Uncertain significance (Nov 27, 2023)	2634708
10-104131414-T-C	not specified • CFAP43-related disorder	Uncertain significance (Aug 17, 2021)	2350814
10-104132169-G-C		Benign/Likely benign (Jan 01, 2024)	709932
10-104132174-T-C		Benign (Dec 31, 2019)	717165
10-104133651-T-C	not specified	Uncertain significance (May 24, 2024)	3266442
10-104133710-C-T	Normal pressure hydrocephalus	Pathogenic (Jan 27, 2020)	805993
10-104140589-TGAGCTCAGGAGTTTGAGAACAGCCTGGGCAACATATTAAGACTCTGTTTTTACAAAAAACTAATTTTAAAACAATTAGCTGGGTGTGGTGGTGTGAACCTGTACTCCCAGCTACTTGGGAGGTGAAGGTGGGAGGATCTATTGAGCCTAGCTAAGGGTTAAGGCTGCAGTGAGCCATGATTGTGCCACAAGACTCTAGCCTGAGTAACAAAGCAAGACCTTGAATTAAAATAAAAATAAAAAGTATAATTACCCGAATCACAGAATTCAAGTCTTCAATTATGTTCTTGTTGATGAGAATTGCATCAGAATACTCCAGTACTAGCTGGAAATTTTCCAGTTCTACTTGTCCTTGTTTAAGAAGAATTTGGATTGTCAAATTCAACTGGAATCTCACTTTCTCTTCCTGTAATCTGAATTGAAAAGTACTTCAAAGCAAGTAGTTGTAATATATTTCAAATTTCACCTATTATCTGAGAATATAAAAATCGAATCAGCTTAAGGAAAACATGCTGGAGATTAGTGTGGAGAATATTTTCCTGATGATGAGCTTTCCTAGAGGTCTCTCTGAAACCTCTTCCTATTGATGCAGAATTATACCTGGGTTGCTCAAAAAATGGTATGGACAGAAATACATTTATAGATTTTTACTTTAGGATTAAGAAAAGATTGTATAATTTTGACGGTAATAAAAGTAAAGTAAAAATGAAGAAAATAGAGACACTTTTAAATAACAAATCTGGCCAGGCGCAGTGGCTCATGCCTGTAATCCCAGCATTTTGGGATGCCGAGGTGGGTGGATCATCTGAGGTCAGGAGTTCGAGACTAGCCTGGCCAACATGGCGAAACCCCATCTCTACTAACAATACAAAAATTAGCCAGGGGTGGTGACAGGCACCTGTAATCCCAGCTGCTTGGGAGGCTGAGGCATGAGATCTCTTGAACCTGGGAGGTGGAGACTGCAGTGAGCCCAGATCGTGCCACTGCACTCCAGCTTGTGTGACAGAGTGAGGCTCCATTTCAAAATAAATAAATAAATAAATAAAATAACTCTATTAAAATTCTGAACTTATTTATTGATTTCTGATACTATACTAACAATATTTAATATGTAAGTTACTTAACAAATCTATTTCTGGGTAATTCATATCCTCGCTATAGCCTAGATCTAAAAATGATGTGTTCTCAATGAATTTGGGAACATCAGAGAAGTATTTATCGATGAGGCTATAAATATAGCCAAAAAATGAAGCAAGGACTTAAATATCTTAATCACTTAGTAAACAACAAGTTCCCCTAAAGAAAAATATATCAGTTGGCTGCGTGTCTACATGGAAAGTTCTTAGACATCTGCTTAATTTTCCACATGGTTAGCTTATATGCCTTGAGCCCCAAAGTACTGAAAAACAGGTTCTTTGTATTTTTATGTGGAAGGGGCCGACTTAAAACAATACTAAGATTTTTCTGAAACTTGCTTATTTGTAATAAGAGCAACAAAACGTGGGAAAGTTCCATCCTGAATCAAGGTCTATGTAACAAAGCAGGCTTTTTAAAATAGAAATTTTAAAGCACAGTGCTGGAAGGGAGATGGCTGTAAAGCAGTCAGTAGGCATTCTCCCCAGTGATAACACAACCTGATTTAGCCCTAATTAGACTTTGAATAGGTGAACATGAAAGAAAGCTTCAAATTACAGGATGAGTTCATGGAACACTCTCTCAATCTCCTGTTGCACCTTCTCTTCCTCCTCAACTCTCTTCTGGAGGAAAGTTGCCATTTCCAATAAGTCAGCTGCTTTCTGCTTTACCTAAAGAAACCAAGCCAGAAACATGTCAGAACATATGGAGCTTCAATTTTAGACAACATACATCTTTTAACTTTTTAAATTTAAAAACCTTAACAGGTCTATCTTTCGAAGAAAGTAATAAAACATTTAAATTTAAATGTCTAAAACTTACATGGTATGTAACAATTTGAACGATTTGAAAGTATCAAATTTGCTTCTTGGTGAAAATCAAGTATGCAGGCAACTATAAATTCTTTTATATCTTATTTTTAAAATTTGTTCTCATCACTTTAAGTGAAATTATAGAATCCTAGGTACTTTAACAAAAATATGCCAGCCTGATGCATGTGGGCATTAAATTTAGGGAATTTGGGGTAGTGGTCAAGAAGCAACAAGAGGAAGGATTCTCTTCCCAAATAAAGACCCTCTTAAATTTTTACTCGTTGCCACATTCTAGCAAAACTATAAAGTTGGTTCTGCTGAGCCAAATATAATTCTAATCTATGCAAAATGAGATAACCTACAACAGTGCTGTCCAAGAAAAATATAACGTGAGCCATAAATGTGAGTCACATATGTAATTTTAAATTCTGTAGTAGCCGCATTATAAAAAGTGAAATCAAAGAAATGAACTTAATTTTACTAATATATTTTAATTAAATGTATCCAGAATATTATCACTTCAACCTATAATCAATATAAAAATATTAATGAGACATATTTCTTTTTGTTCATACTAAGCCTTCTAATGTGTATGTTTTCCACTTACAGCACATCTCAGTTAGGACTGGCAATATTTATTTCAAATGCATAATAACCACTTGTGGCTAATGGACACTATTTTGAACGGCACCAGTCTAAAAGCAACAGGCCTACACTTAGCCTTCAATAGCACCAGGGTTAATATAGTATTTCATTATCTTATTACTATGACCAAATACTACCCTAGCAGGGAAACCTAAATAATTAGCTTTTTTGGTTACACTGACCAATGTAAACTATGTATTTGATATTAGTACACTAAAAATTAAATTAAGTTAAAATAGTATATACTTTCTGTTCATTTTCCACTTTTGCTCGTCTTGTCATGCAGAAATGATTCCAGACCAAAGGGTCCAAGCCTTCTGGCATGTTACTAATATTGTCCAACTCATCCATAGCTTTCATTAACTGGGCAAAGGCATCCTTATTCAACTTGCCAGATCCTGGTAGTTCTCCGAAAGGGACAACGCTGGTTGTTTCTGAGTGCGTTTTCTGTTTGGAAATCCTGGTATTACCAAGAAAAGCCCATCAACATTTCACATTCTCATAAAAACATCAATGTGAAACAATTAGGCCCTTAGCACAGGCATAACACATTGTATGGCTCTTCCCTTTGCCATGTGATGGCTGGTAGGTGGGTTATTCCACAGATAAAGGGATCCACTTTGCCCTTCTTCCATACTCTCCAGGTTCTCAGACGTGACCTTGGCTAGACTACAGATGTCTCCAACTATTGTCAGCACTGACAGACAATTGTGTCTGTGCTAG-T	Spermatogenic failure 19	Pathogenic (Jul 25, 2017)	430937
10-104140843-C-T	CFAP43-related disorder	Likely benign (Dec 13, 2018)	725604
10-104140844-G-A	not specified	Uncertain significance (Sep 19, 2022)	2400138
10-104140889-T-C	not specified	Uncertain significance (Aug 22, 2022)	2308737
10-104140974-C-T	CFAP43-related disorder	Benign (Jul 10, 2019)	3056592
10-104142313-C-T	CFAP43-related disorder	Likely benign (Apr 09, 2019)	3052061
10-104142353-A-G	not specified	Uncertain significance (May 06, 2022)	2220441
10-104143450-T-G	CFAP43-related disorder	Likely benign (Jun 12, 2019)	3034143
10-104143452-G-A	Spermatogenic failure 19	Pathogenic (Jul 25, 2017)	430934
10-104143495-T-G	not specified	Uncertain significance (Sep 16, 2021)	2352589
10-104143571-C-T	not specified	Uncertain significance (Oct 25, 2022)	2384621
10-104143598-A-T	not specified	Uncertain significance (Jan 20, 2023)	2476873
10-104143611-T-C	not specified	Uncertain significance (Aug 09, 2021)	2241512
10-104145482-C-T	not specified	Uncertain significance (Mar 15, 2024)	3266435
10-104145483-G-A	Normal pressure hydrocephalus	Likely pathogenic (-)	2585282

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP43	protein_coding	protein_coding	ENST00000357060	38	102475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-22	1.00	125449	0	299	125748	0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.773	781	844	0.925	0.0000434	11027
Missense in Polyphen		173	196.85	0.87886		2703
Synonymous	0.350	304	312	0.975	0.0000175	2933
Loss of Function	3.94	51	91.8	0.556	0.00000447	1218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00214	0.00213
Ashkenazi Jewish	0.00	0.00
East Asian	0.00648	0.00649
Finnish	0.000371	0.000370
European (Non-Finnish)	0.000851	0.000844
Middle Eastern	0.00648	0.00649
South Asian	0.000725	0.000719
Other	0.000818	0.000815

dbNSFP

Source: dbNSFP

Function: FUNCTION: Flagellar protein involved in sperm flagellum axoneme organization and function. {ECO:0000250|UniProtKB:E9Q7R9}.;

Recessive Scores

pRec: 0.0794

Intolerance Scores

loftool
rvis_EVS: -1.46
rvis_percentile_EVS: 3.76

Haploinsufficiency Scores

pHI: 0.120
hipred: N
hipred_score: 0.266
ghis: 0.450

Mouse Genome Informatics

Gene name: Cfap43
Phenotype: reproductive system phenotype; cellular phenotype;

Gene ontology

Biological process: sperm axoneme assembly
Cellular component: axoneme;motile cilium
Molecular function