CFAP92

cilia and flagella associated protein 92 (putative)

Basic information

Region (hg38): 3:128909866-129002690

Previous symbols: [ "KIAA1257" ]

Links

ENSG00000114656 ∙ NCBI:57501 ∙ ∙ HGNC:29231 ∙ Uniprot:Q9ULG3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP92 gene.

• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP92 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	3	19	35	118	8	183
Total	3	19	57	122	8

Variants in CFAP92

This is a list of pathogenic ClinVar variants found in the CFAP92 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-128909880-A-G			Likely benign (Jun 28, 2018)
3-128909966-A-G			Benign (Jun 14, 2018)
3-128909970-G-A			Benign (Sep 01, 2023)
3-128910005-G-C			Likely benign (Apr 02, 2023)
3-128910005-G-T			Likely benign (Dec 31, 2022)
3-128910006-C-A			Likely benign (Aug 04, 2023)
3-128910007-C-T			Likely benign (Sep 25, 2023)
3-128910009-C-T			Likely benign (Mar 20, 2023)
3-128910010-T-C			Likely benign (May 17, 2023)
3-128910011-G-A			Likely benign (Nov 06, 2023)
3-128910014-A-C			Likely benign (Jun 11, 2023)
3-128910014-ATCCCAGACCATC-A			Pathogenic (Sep 08, 2023)
3-128910015-T-A			Likely benign (Jun 15, 2023)
3-128910017-C-G			Likely benign (May 05, 2022)
3-128910017-C-T			Likely benign (Dec 04, 2023)
3-128910021-A-G		ACAD9-related disorder	Uncertain significance (Mar 21, 2024)
3-128910022-C-CCAT			Uncertain significance (Jul 04, 2022)
3-128910025-T-C			Uncertain significance (Jul 15, 2022)
3-128910032-G-A			Likely benign (Nov 09, 2021)
3-128910035-G-A			Likely benign (May 23, 2019)
3-128910050-G-A			Likely benign (Apr 06, 2021)
3-128910051-C-T		Acyl-CoA dehydrogenase 9 deficiency • Mitochondrial complex I deficiency	Pathogenic/Likely pathogenic (Mar 04, 2024)
3-128910051-CG-C		Acyl-CoA dehydrogenase 9 deficiency	Likely pathogenic (Jan 19, 2023)
3-128910052-G-A		Acyl-CoA dehydrogenase 9 deficiency	Likely pathogenic (Sep 26, 2023)
3-128910053-G-C		Acyl-CoA dehydrogenase 9 deficiency	Likely benign (Jan 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP92	protein_coding	protein_coding	ENST00000265068	7	92825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.17e-9	0.185	124601	0	196	124797	0.000786

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.558	203	227	0.896	0.0000125	2689
Missense in Polyphen		48	56.853	0.84428		742
Synonymous	0.530	87	93.5	0.930	0.00000635	744
Loss of Function	0.495	15	17.2	0.871	8.11e-7	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000698	0.000692
Ashkenazi Jewish	0.00	0.00
East Asian	0.00235	0.00232
Finnish	0.0000931	0.0000927
European (Non-Finnish)	0.000538	0.000531
Middle Eastern	0.00235	0.00232
South Asian	0.00217	0.00216
Other	0.00117	0.00115

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0810

Intolerance Scores

• loftool: 0.246
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.06

Haploinsufficiency Scores

• pHI: 0.0597
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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