CFAP44

cilia and flagella associated protein 44, the group of Cilia and flagella associated|MicroRNA protein coding host genes|WD repeat domain containing

Basic information

Region (hg38): 3:113286930-113441610

Previous symbols: [ "WDR52" ]

Links

ENSG00000206530 ∙ NCBI:55779 ∙ OMIM:617559 ∙ HGNC:25631 ∙ Uniprot:Q96MT7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 20 (Moderate), mode of inheritance: AR
• non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 20	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 CFAP44 gene.

• not provided (3 variants)
• Spermatogenic failure 20 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP44 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				27	6	33
missense			56	10	8	74
nonsense	3	2		1		6
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region				6	2	8
non coding						0
Total	4	3	56	38	14

Highest pathogenic variant AF is 0.000447

Variants in CFAP44

This is a list of pathogenic ClinVar variants found in the CFAP44 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-113291569-G-A			Likely benign (Jul 16, 2018)
3-113291580-C-CTT		CFAP44-related disorder	Likely pathogenic (Mar 06, 2024)
3-113291587-T-C			Likely benign (Apr 01, 2023)
3-113291589-G-A			Likely benign (Dec 31, 2019)
3-113291671-C-T		CFAP44-related disorder	Likely benign (Feb 22, 2019)
3-113291677-G-C			Likely benign (Jul 26, 2018)
3-113291704-T-C		CFAP44-related disorder	Benign (Dec 31, 2019)
3-113291738-A-G		CFAP44-related disorder	Uncertain significance (Mar 12, 2024)
3-113294787-A-G			Uncertain significance (Jun 01, 2021)
3-113294794-G-A			Likely benign (Dec 19, 2018)
3-113296800-A-T			Benign (Dec 31, 2019)
3-113296840-C-T		Inborn genetic diseases	Uncertain significance (Jul 01, 2023)
3-113304042-G-A		CFAP44-related disorder	Benign (Dec 31, 2019)
3-113305051-C-T			Likely benign (Aug 01, 2022)
3-113305102-A-C			Benign (Aug 15, 2018)
3-113305155-G-A			Benign (Jun 25, 2020)
3-113308168-A-G			Likely benign (Apr 01, 2022)
3-113326453-C-T		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
3-113326478-G-A			Benign (Dec 31, 2019)
3-113326483-A-T		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
3-113326613-T-C		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
3-113326638-C-A			Benign (Dec 31, 2019)
3-113330176-C-T			Uncertain significance (Jul 01, 2023)
3-113330197-C-G		Inborn genetic diseases	Likely benign (Jul 26, 2021)
3-113330197-C-T			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP44	protein_coding	protein_coding	ENST00000393845	34	154681

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.10e-15	1.00	125576	0	172	125748	0.000684

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	801	918	0.873	0.0000462	12303
Missense in Polyphen		168	208.86	0.80436		2844
Synonymous	1.41	284	316	0.899	0.0000162	3306
Loss of Function	5.12	41	94.8	0.432	0.00000547	1221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00163	0.00162
Ashkenazi Jewish	0.00616	0.00617
East Asian	0.00158	0.00147
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000338	0.000334
Middle Eastern	0.00158	0.00147
South Asian	0.000131	0.000131
Other	0.000991	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Flagellar protein involved in sperm flagellum axoneme organization and function. {ECO:0000250|UniProtKB:E9Q5M6}.

Intolerance Scores

• rvis_EVS: 2.43
• rvis_percentile_EVS: 98.54

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.372
• ghis: 0.427

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap44
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: sperm axoneme assembly;cilium-dependent cell motility
• Cellular component: cytoplasm;cytoskeleton;motile cilium