CFAP92

Summary

CFAP92 (cilia and flagella associated protein 92 (putative), HGNC:29231) is a protein-coding gene on chromosome 3q21.3, encoding Uncharacterized protein CFAP92 (Q9ULG3).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 163 total — 6 likely-pathogenic
• MANE Select transcript: NM_001394090

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29231
Approved symbol	CFAP92
Name	cilia and flagella associated protein 92 (putative)
Location	3q21.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ43738, FAP92
Ensembl gene	ENSG00000114656
Ensembl biotype	protein_coding
Entrez	57501

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000265068, ENST00000507225, ENST00000510149, ENST00000511204, ENST00000511438, ENST00000515659, ENST00000637488, ENST00000645291, ENST00000669741

RefSeq mRNA: 6 — MANE Select: NM_001394090 NM_001348520, NM_001348521, NM_001348522, NM_001348523, NM_001394090, NM_020741

CCDS: CCDS46905, CCDS87133, CCDS93370

Canonical transcript exons

ENST00000645291 — 16 exons

Exon	Start	End
ENSE00000778077	128993043	128993336
ENSE00001367608	128935125	128935319
ENSE00001370307	128915357	128915563
ENSE00001372457	128915119	128915275
ENSE00002042312	128909873	128910333
ENSE00002087056	128971287	128971433
ENSE00003533688	128988728	128988918
ENSE00003575486	128978045	128978185
ENSE00003579094	128976979	128977066
ENSE00003616840	128987616	128987829
ENSE00003652626	128975779	128975903
ENSE00003797375	128916107	128916271
ENSE00003799892	128932700	128932997
ENSE00003818400	128945071	128945975
ENSE00003820191	128965511	128965695
ENSE00003934509	128993980	128994076

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 88.30.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5833 / max 156.9402, expressed in 426 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
44472	0.8568	259
44473	0.2824	114
44477	0.2299	98
44476	0.0633	23
44478	0.0576	17
44475	0.0539	25
44474	0.0395	13

Top tissues by expression

245 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	88.30	gold quality
right testis	UBERON:0004534	87.66	gold quality
testis	UBERON:0000473	86.56	gold quality
sperm	CL:0000019	85.64	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.58	gold quality
secondary oocyte	CL:0000655	83.29	gold quality
oocyte	CL:0000023	81.79	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.03	gold quality
right uterine tube	UBERON:0001302	78.71	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	73.91	gold quality
blood	UBERON:0000178	73.15	gold quality
islet of Langerhans	UBERON:0000006	72.83	gold quality
colonic epithelium	UBERON:0000397	72.74	gold quality
bone marrow cell	CL:0002092	72.33	silver quality
adenohypophysis	UBERON:0002196	72.08	gold quality
pituitary gland	UBERON:0000007	71.69	gold quality
sural nerve	UBERON:0015488	70.32	gold quality
prefrontal cortex	UBERON:0000451	69.61	gold quality
right frontal lobe	UBERON:0002810	69.42	gold quality
right hemisphere of cerebellum	UBERON:0014890	68.90	gold quality
mammary duct	UBERON:0001765	68.89	gold quality
calcaneal tendon	UBERON:0003701	68.21	gold quality
cerebellar hemisphere	UBERON:0002245	68.08	gold quality
hypothalamus	UBERON:0001898	68.01	gold quality
cerebellar cortex	UBERON:0002129	68.01	gold quality
nucleus accumbens	UBERON:0001882	67.96	gold quality
left ovary	UBERON:0002119	67.78	gold quality
skin of abdomen	UBERON:0001416	67.76	gold quality
Brodmann (1909) area 9	UBERON:0013540	67.69	gold quality
lower esophagus mucosa	UBERON:0035834	67.59	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting CFAP92, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-4786-3P	99.36	68.35	1390
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-8065	99.19	70.38	1289
HSA-MIR-384	98.71	67.34	1229
HSA-MIR-410-5P	96.55	66.28	459
HSA-MIR-323B-5P	96.12	66.39	472
HSA-MIR-6815-5P	96.05	65.55	662
HSA-MIR-6865-5P	96.05	65.58	675
HSA-MIR-494-5P	95.31	66.29	463
HSA-MIR-3679-5P	94.75	66.46	862
HSA-MIR-1185-5P	94.47	65.95	725

Literature-anchored findings (GeneRIF, showing 1)

• The gain of function studies indicated that KIAA1257 activate NR5A1 gene expression. (PMID:18579725)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap92	ENSDARG00000052912
mus_musculus	Cfap92	ENSMUSG00000089997
rattus_norvegicus	Cfap92	ENSRNOG00000031408

Protein

Protein identifiers

Uncharacterized protein CFAP92 — Q9ULG3 (reviewed: Q9ULG3)

Alternative names: Putative cilia and flagella associated protein 92

All UniProt accessions (5): A0A1B0GVL5, A0A2R8YFM9, A0A590UJZ5, Q9ULG3, D6RH05

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q9ULG3-1	1	yes
Q9ULG3-2	2

RefSeq proteins (6): NP_001335449, NP_001335450, NP_001335451, NP_001335452, NP_001381019, NP_065792 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027876	DUF4550	Domain

Pfam: PF15084

UniProt features (11 total): compositionally biased region 6, region of interest 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULG3-F1	57.39	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): chr3q21, DODD_NASOPHARYNGEAL_CARCINOMA_DN, DLX6_TARGET_GENES, ZNF610_TARGET_GENES, MIR5688, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2, MIR3605_5P, GAO_ESOPHAGUS_25W_C1_CILIATED_EPITHELIAL_CELLS, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_LIVER_HEMATOPOIETIC_STEM_CELLS, ZNF623_TARGET_GENES, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_6H_ACT_CD4_TCELL_UP, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_24H_ACT_CD4_TCELL_DN, GSE2706_LPS_VS_R848_AND_LPS_2H_STIM_DC_UP, GSE9509_LPS_VS_LPS_AND_IL10_STIM_IL10_KO_MACROPHAGE_30MIN_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1391 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP92	CCDC180	Q9P1Z9	667
CFAP92	SPATA17	Q96L03	605
CFAP92	DLEC1	Q9Y238	572
CFAP92	SPAG17	Q6Q759	520
CFAP92	RNF39	Q9H2S5	515
CFAP92	LRRC72	A6NJI9	514
CFAP92	SPAG6	O75602	464
CFAP92	LHFPL7	Q6ICI0	445
CFAP92	FBXO46	Q6PJ61	419
CFAP92	C1D	Q13901	417
CFAP92	CFAP221	Q4G0U5	417
CFAP92	WBP2NL	Q6ICG8	370
CFAP92	SNRNP27	Q8WVK2	360
CFAP92	HYDIN	Q4G0P3	353
CFAP92	NIBAN1	Q9BZQ8	351

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CRY1	IGKV2D-30	psi-mi:“MI:0914”(association)	0.350

BioGRID (4): KIAA1257 (Positive Genetic), VAMP3 (Cross-Linking-MS (XL-MS)), KIAA1257 (Co-fractionation), KIAA1257 (Affinity Capture-RNA)

ESM2 similar proteins: A0JM13, A2RRS8, B0DOB4, D3YYM4, E2RK09, O15259, P79457, Q14596, Q3MJ13, Q3ULW6, Q3V0L5, Q4AC94, Q501R9, Q52KB6, Q5F479, Q5FW46, Q5RC94, Q5RFQ4, Q5SUS0, Q5VX52, Q5XI03, Q5XIR4, Q5XX13, Q5ZI58, Q6AY22, Q6IRU7, Q6P1H6, Q6P4T1, Q6ZPF3, Q7TP65, Q86T82, Q8BFU3, Q8BVV7, Q8C0R0, Q8IVF5, Q8IW35, Q8N5R6, Q8ND24, Q8NDB2, Q91XT6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

163 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	6
Uncertain significance	122
Likely benign	20
Benign	1

Top pathogenic / likely-pathogenic (6)

Variant ID	HGVS	Classification
1932297	NM_014049.5(ACAD9):c.1692+1G>A	Likely pathogenic
242459	NM_014049.5(ACAD9):c.1595G>A (p.Arg532Gln)	Likely pathogenic
3240617	NM_014049.5(ACAD9):c.1799_1800del (p.Lys600fs)	Likely pathogenic
3240684	NM_014049.5(ACAD9):c.1690G>A (p.Glu564Lys)	Likely pathogenic
3588368	NM_014049.5(ACAD9):c.1564-2A>G	Likely pathogenic
432152	NM_014049.5(ACAD9):c.1693-2A>G	Likely pathogenic

SpliceAI

4087 predictions. Top by Δscore:

Variant	Effect	Δscore
3:128910019:A:AG	acceptor_gain	1.0000
3:128910020:G:GG	acceptor_gain	1.0000
3:128910149:GGT:G	donor_loss	1.0000
3:128910150:GTGAG:G	donor_loss	1.0000
3:128910151:T:G	donor_loss	1.0000
3:128910729:C:CA	acceptor_gain	1.0000
3:128910730:G:A	acceptor_gain	1.0000
3:128910812:GT:G	donor_gain	1.0000
3:128910814:G:GG	donor_gain	1.0000
3:128912505:A:AG	acceptor_gain	1.0000
3:128912506:G:GG	acceptor_gain	1.0000
3:128915347:C:A	donor_gain	1.0000
3:128915365:G:C	donor_gain	1.0000
3:128916101:TCTCA:T	donor_loss	1.0000
3:128916102:CTCAC:C	donor_loss	1.0000
3:128916103:TCACC:T	donor_loss	1.0000
3:128916104:CACC:C	donor_loss	1.0000
3:128916105:ACCTT:A	donor_loss	1.0000
3:128916106:C:CT	donor_loss	1.0000
3:128916267:TTTTT:T	acceptor_gain	1.0000
3:128916268:TTTT:T	acceptor_gain	1.0000
3:128916269:TTT:T	acceptor_gain	1.0000
3:128916270:TT:T	acceptor_gain	1.0000
3:128916271:TCTGA:T	acceptor_loss	1.0000
3:128916272:C:CC	acceptor_gain	1.0000
3:128916272:CT:C	acceptor_loss	1.0000
3:128916273:T:C	acceptor_loss	1.0000
3:128935120:CCCA:C	donor_loss	1.0000
3:128935121:CCA:C	donor_loss	1.0000
3:128935123:A:AT	donor_loss	1.0000

AlphaMissense

7309 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:128987787:A:G	W166R	0.997
3:128987787:A:T	W166R	0.997
3:128987796:A:G	W163R	0.996
3:128987796:A:T	W163R	0.996
3:128978170:A:T	V228D	0.991
3:128988756:G:T	A142D	0.991
3:128987785:C:A	W166C	0.989
3:128987785:C:G	W166C	0.989
3:128987794:C:A	W163C	0.989
3:128987794:C:G	W163C	0.989
3:128987817:A:G	W156R	0.989
3:128987817:A:T	W156R	0.989
3:128988777:A:T	I135K	0.988
3:128988820:A:C	Y121D	0.988
3:128993063:A:G	L81P	0.988
3:128987747:A:G	L179S	0.985
3:128988757:C:G	A142P	0.985
3:128988752:T:A	K143N	0.984
3:128988752:T:G	K143N	0.984
3:128993069:A:T	I79N	0.984
3:128993075:A:G	F77S	0.984
3:128988767:A:C	F138L	0.983
3:128988767:A:T	F138L	0.983
3:128988769:A:G	F138L	0.983
3:128987786:C:G	W166S	0.982
3:128993067:A:G	S80P	0.981
3:128993060:G:T	A82D	0.980
3:128988746:G:C	F145L	0.979
3:128988746:G:T	F145L	0.979
3:128988748:A:G	F145L	0.979

dbSNP variants (sampled 300 via entrez): RS1000019125 (3:129002914 C>T), RS1000102469 (3:128936798 T>G), RS1000115861 (3:128982778 T>G), RS1000151926 (3:128926799 A>G), RS1000164613 (3:128923996 A>C), RS1000188260 (3:128961551 A>G), RS1000213318 (3:129015607 C>T), RS1000245625 (3:129026466 C>G), RS1000246342 (3:128961882 A>G,T), RS1000294120 (3:128948097 G>A,T), RS1000316873 (3:128984526 G>A,T), RS1000322764 (3:129026116 G>A,C,T), RS1000329326 (3:128916754 C>G), RS1000335010 (3:128984460 G>A), RS1000350741 (3:128929880 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:611126

GenCC curated gene-disease

Mondo (1): acyl-CoA dehydrogenase 9 deficiency (MONDO:0012624)

Orphanet (1): Acyl-CoA dehydrogenase 9 deficiency (Orphanet:99901)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003649_7	Pneumococcal bacteremia	5.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:1001925	pneumococcal bacteremia

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C567006	Acyl-CoA Dehydrogenase Family, Member 9, Deficiency of (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	3
sotorasib	affects cotreatment, decreases expression	1
propionaldehyde	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Lipopolysaccharides	affects response to substance, increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.