CFAP92

Gene

cilia and flagella associated protein 92 (putative)

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

KIAA1257

MANE transcript

NM_001394090.1

Inheritance

—

ClinVar variants

P:1U:57B:9

Top phenotype

Acyl-CoA dehydrogenase 9 deficiency

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr3:128,909,866-129,002,690

External References & Databases

Ensembl (ENSG00000114656)

Transcript & Mutation Effects

hg38 • Region Span ~92.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CFAP92 variants in ClinVar

6 Conditions Cataloged

not providedTotal: 104

not specifiedTotal: 72

Acyl-CoA dehydrogenase 9 deficiencyTotal: 34

Inborn genetic diseasesTotal: 9

ACAD9-related disorderTotal: 2

Mitochondrial complex I deficiencyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394090.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			54 clinvar	5 clinvar		59
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)		1 clinvar	3 clinvar			4
Total	0	1	57	9	0	67

Highest pathogenic variant AF is 0.000021065858

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394090.1	RefSeq	NP_001381019.1	15	MANE Select
ENST00000645291.3	Ensembl	ENSP00000496592.2	15	MANE Select
NM_001348520.2	RefSeq	NP_001335449.1	11	Standard
NM_001348521.2	RefSeq	NP_001335450.1	11	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265068
Coding exons: 7
Length: 92825
Individuals with no LoFs: 124601
Homozygous LoFs: 0
Heterozygous LoFs: 196
Defined: 124797
p: 0.000786

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.558	203	227	0.896	0.0000125	2689
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0024	0.0023	notable
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00054	0.00053	rare
South Asian	0.0022	0.0022	notable
Other	0.0012	0.0012	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0810

Intolerance Scores

LoFtool: 0.246
RVIS EVS: 0.95
RVIS percentile EVS: 90.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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