CFAP90

Summary

CFAP90 (cilia and flagella associated protein 90, HGNC:27028) is a protein-coding gene on chromosome 5p15.31, encoding Cilia- and flagella-associated protein 90 (A4QMS7). Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating.

Predicted to be involved in flagellated sperm motility. Located in axoneme and ciliary basal body.

Source: NCBI Gene 134121 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total — 1 pathogenic
• MANE Select transcript: NM_001089584

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27028
Approved symbol	CFAP90
Name	cilia and flagella associated protein 90
Location	5p15.31
Locus type	gene with protein product
Status	Approved
Aliases	LOC134121
Ensembl gene	ENSG00000215217
Ensembl biotype	protein_coding
Entrez	134121

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000399810, ENST00000509627, ENST00000872898, ENST00000872899, ENST00000872900, ENST00000872901, ENST00000872902, ENST00000956397

RefSeq mRNA: 1 — MANE Select: NM_001089584 NM_001089584

CCDS: CCDS43300

Canonical transcript exons

ENST00000399810 — 3 exons

Exon	Start	End
ENSE00001540263	7830378	7832029
ENSE00001540272	7835382	7835498
ENSE00001540276	7850875	7851133

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 98.52.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0866 / max 146.1632, expressed in 421 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60865	1.9057	397
60866	0.1810	89

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	98.52	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.97	gold quality
bronchial epithelial cell	CL:0002328	93.45	gold quality
bronchus	UBERON:0002185	91.66	gold quality
right testis	UBERON:0004534	89.27	gold quality
left testis	UBERON:0004533	89.22	gold quality
oviduct epithelium	UBERON:0004804	87.74	gold quality
mucosa of paranasal sinus	UBERON:0005030	86.30	gold quality
testis	UBERON:0000473	85.70	gold quality
fallopian tube	UBERON:0003889	84.35	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.92	gold quality
sperm	CL:0000019	83.14	gold quality
hypothalamus	UBERON:0001898	81.96	gold quality
anterior cingulate cortex	UBERON:0009835	81.29	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.16	gold quality
amygdala	UBERON:0001876	79.70	gold quality
adenohypophysis	UBERON:0002196	79.21	gold quality
ventricular zone	UBERON:0003053	78.85	gold quality
nucleus accumbens	UBERON:0001882	78.58	gold quality
epithelium of nasopharynx	UBERON:0001951	77.55	gold quality
right frontal lobe	UBERON:0002810	77.37	gold quality
caudate nucleus	UBERON:0001873	77.06	gold quality
pituitary gland	UBERON:0000007	76.50	gold quality
prefrontal cortex	UBERON:0000451	75.11	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	74.46	gold quality
right lung	UBERON:0002167	74.43	gold quality
cortical plate	UBERON:0005343	73.13	gold quality
endocervix	UBERON:0000458	72.27	gold quality
nasal cavity mucosa	UBERON:0001826	72.17	gold quality
neocortex	UBERON:0001950	72.13	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-MTAB-10283	yes	1488.27
E-MTAB-10485	yes	462.01
E-CURD-114	yes	64.04
E-HCAD-1	yes	32.47
E-MTAB-10287	yes	27.65
E-GEOD-130148	yes	11.66
E-MTAB-9388	yes	6.72
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

81 targeting CFAP90, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-664B-3P	99.84	71.65	3590

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap90	ENSDARG00000115108
mus_musculus	Cfap90	ENSMUSG00000021534
rattus_norvegicus	Cfap90	ENSRNOG00000047406

Protein

Protein identifiers

Cilia- and flagella-associated protein 90 — A4QMS7 (reviewed: A4QMS7)

All UniProt accessions (2): A4QMS7, D6RHK3

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating.

Subunit / interactions. Microtubule inner protein component of sperm flagellar doublet microtubules.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium axoneme. Flagellum axoneme.

RefSeq proteins (1): NP_001083053* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027901	CFAP90	Family

Pfam: PF15074

UniProt features (5 total): sequence variant 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7UNG	ELECTRON MICROSCOPY	3.6
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A4QMS7-F1	75.84	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 66 (showing top): GOCC_MICROTUBULE_ORGANIZING_CENTER, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOCC_CYTOPLASMIC_REGION, GOCC_MOTILE_CILIUM, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY, DODD_NASOPHARYNGEAL_CARCINOMA_DN, WHITFIELD_CELL_CYCLE_G2, GOCC_AXONEMAL_MICROTUBULE, GOCC_9PLUS2_MOTILE_CILIUM, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER

GO Biological Process (1): flagellated sperm motility (GO:0030317)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (9): axoneme (GO:0005930), ciliary basal body (GO:0036064), sperm flagellum (GO:0036126), axonemal B tubule inner sheath (GO:0160112), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
cilium	2
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
binding	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
microtubule organizing center	1
9+2 motile cilium	1
A axonemal microtubule	1
axonemal microtubule doublet inner sheath	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

246 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP90	PIERCE1	Q5BN46	727
CFAP90	CFAP96	A7E2U8	642
CFAP90	CFAP299	Q6V702	625
CFAP90	CABCOCO1	Q8IVU9	595
CFAP90	IFT57	Q9NWB7	591
CFAP90	CLXN	Q9HAE3	573
CFAP90	ARMC3	Q5W041	524
CFAP90	CFAP184	Q2M329	513
CFAP90	CCDC170	Q8IYT3	488
CFAP90	IQUB	Q8NA54	465
CFAP90	EFCAB7	A8K855	386
CFAP90	ENKUR	Q8TC29	384
CFAP90	CFAP100	Q494V2	358
CFAP90	CCDC40	Q4G0X9	357
CFAP90	CFAP57	Q96MR6	356

IntAct

13 interactions, top by confidence:

A	B	Type	Score
CFAP90	HSF2BP	psi-mi:“MI:0915”(physical association)	0.560
CFAP90	KRT34	psi-mi:“MI:0915”(physical association)	0.560
CFAP90	KRT31	psi-mi:“MI:0915”(physical association)	0.560
CFAP90	CDKN2D	psi-mi:“MI:0915”(physical association)	0.560
CFAP90	HSF2BP	psi-mi:“MI:0915”(physical association)	0.000
CFAP90	KRT34	psi-mi:“MI:0915”(physical association)	0.000
CFAP90	KRT31	psi-mi:“MI:0915”(physical association)	0.000
CDKN2D	CFAP90	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): C5orf49 (Two-hybrid), C5orf49 (Two-hybrid), C5orf49 (Two-hybrid), C5orf49 (Two-hybrid)

ESM2 similar proteins: A0A087WRI3, A2BFC9, A2RRW4, A4QMS7, A6NJV1, A6NL82, A6QPC0, A6QQ68, A8E4X8, A8E5W8, A8QW39, A9JS51, D6REC4, F1P3Y5, G3X6E2, P0C875, Q0VB26, Q1MSJ5, Q2IA00, Q2T9Q3, Q2TA11, Q3UY96, Q494V2, Q497Q6, Q4KKZ1, Q4QR77, Q4R5Y0, Q4R8V8, Q5NC57, Q5ZIH9, Q6J272, Q6PII3, Q6ZQR2, Q6ZVS7, Q7Z4T9, Q8CFW7, Q8N1D5, Q8N6G2, Q8WW14, Q95LR0

Diamond homologs: A4QMS7, Q9DAR0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
915985	GRCh37/hg19 5p15.33-14.3(chr5:71904-22078969)	Pathogenic

SpliceAI

728 predictions. Top by Δscore:

Variant	Effect	Δscore
5:7836339:A:C	donor_gain	1.0000
5:7832028:TC:T	acceptor_gain	0.9900
5:7832028:TCCTG:T	acceptor_loss	0.9900
5:7832029:CC:C	acceptor_gain	0.9900
5:7832030:C:CG	acceptor_loss	0.9900
5:7832031:T:A	acceptor_loss	0.9900
5:7835376:TATTA:T	donor_loss	0.9900
5:7835377:ATTAC:A	donor_loss	0.9900
5:7835378:TTACC:T	donor_loss	0.9900
5:7835379:TACC:T	donor_loss	0.9900
5:7835380:ACC:A	donor_loss	0.9900
5:7835381:C:CG	donor_loss	0.9900
5:7835381:CCT:C	donor_gain	0.9900
5:7835383:T:TA	donor_gain	0.9900
5:7836349:T:TA	donor_gain	0.9900
5:7837187:T:C	donor_gain	0.9900
5:7850843:T:TA	donor_gain	0.9900
5:7832026:GTTC:G	acceptor_gain	0.9800
5:7832027:TTC:T	acceptor_gain	0.9800
5:7832030:C:CC	acceptor_gain	0.9800
5:7832033:G:C	acceptor_gain	0.9800
5:7832033:G:GC	acceptor_gain	0.9800
5:7835495:CTGT:C	acceptor_gain	0.9800
5:7836338:A:AC	donor_gain	0.9800
5:7850867:GTCCT:G	donor_loss	0.9800
5:7850869:CCTCA:C	donor_loss	0.9800
5:7850870:CTCAC:C	donor_loss	0.9800
5:7850871:TCACC:T	donor_loss	0.9800
5:7850872:CACC:C	donor_loss	0.9800
5:7850873:A:C	donor_loss	0.9800

AlphaMissense

960 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:7835421:T:A	R75S	0.972
5:7835421:T:G	R75S	0.972
5:7850938:G:C	F28L	0.957
5:7850938:G:T	F28L	0.957
5:7850940:A:G	F28L	0.957
5:7832018:C:A	R92S	0.956
5:7832018:C:G	R92S	0.956
5:7831913:G:C	F127L	0.942
5:7831913:G:T	F127L	0.942
5:7831915:A:G	F127L	0.942
5:7835431:C:G	R72P	0.935
5:7835435:G:C	H71D	0.932
5:7831986:C:T	G103E	0.929
5:7835466:A:C	F60L	0.928
5:7835466:A:T	F60L	0.928
5:7835468:A:G	F60L	0.928
5:7835422:C:G	R75T	0.925
5:7850935:G:C	S29R	0.924
5:7850935:G:T	S29R	0.924
5:7850937:T:G	S29R	0.924
5:7835424:G:C	D74E	0.922
5:7835424:G:T	D74E	0.922
5:7831986:C:A	G103V	0.920
5:7835398:A:G	L83P	0.920
5:7832027:T:A	E89D	0.913
5:7832027:T:G	E89D	0.913
5:7831987:C:A	G103W	0.911
5:7835422:C:A	R75I	0.910
5:7831871:A:C	F141L	0.909
5:7831871:A:T	F141L	0.909

dbSNP variants (sampled 300 via entrez): RS1000327017 (5:7842235 T>A), RS1000476851 (5:7843926 G>A), RS1000480952 (5:7832100 C>G), RS1000533331 (5:7832360 T>A,C), RS1000567447 (5:7831467 A>G), RS1001166810 (5:7843324 G>T), RS1001222895 (5:7847558 C>T), RS1001573365 (5:7836392 C>T), RS1001630494 (5:7830837 G>A,T), RS1001657740 (5:7847778 G>A), RS1001663226 (5:7831100 C>G,T), RS1001805911 (5:7849473 C>T), RS1001829467 (5:7837495 TAGG>T), RS1001861419 (5:7832654 G>GTT), RS1001874382 (5:7837557 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:123450

GenCC curated gene-disease

Mondo (1): Cri-du-chat syndrome (MONDO:0007404)

Orphanet (1): Monosomy 5p syndrome (Orphanet:281)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D003410	Cri-du-Chat Syndrome	C10.597.606.360.180; C16.131.077.262; C16.131.260.190; C16.320.180.190

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01238250	Not specified	RECRUITING	Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight
NCT02381457	Not specified	COMPLETED	SNP-based Microdeletion and Aneuploidy RegisTry (SMART)
NCT06740162	Not specified	RECRUITING	Physical Activity and Community EmPOWERment Project