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.

• Inborn_genetic_diseases (118 variants)
• not_provided (63 variants)
• CFAP44-related_disorder (20 variants)
• Spermatogenic_failure_20 (12 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. These statistics are base on transcript: NM_001164496.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				27	8	35
missense	1		107	20	8	136
nonsense	4	2		1		7
start loss						0
frameshift	3	2		1		6
splice donor/acceptor (+/-2bp)	1	2				3
Total	9	6	107	49	16

Highest pathogenic variant AF is 0.000156137

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