CFAP100

Summary

CFAP100 (cilia and flagella associated protein 100, HGNC:26842) is a protein-coding gene on chromosome 3q21.3, encoding Cilia- and flagella-associated protein 100 (Q494V2). May play a role in ciliary/flagellar motility by regulating the assembly and the activity of axonemal inner dynein arm.

Predicted to enable dynein complex binding activity. Predicted to be involved in cilium movement and inner dynein arm assembly. Located in ciliary basal body.

Source: NCBI Gene 348807 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 119 total
• MANE Select transcript: NM_182628

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26842
Approved symbol	CFAP100
Name	cilia and flagella associated protein 100
Location	3q21.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40083, MIA1
Ensembl gene	ENSG00000163885
Ensembl biotype	protein_coding
Entrez	348807

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000352312, ENST00000503905, ENST00000505024, ENST00000506204, ENST00000507830, ENST00000508140, ENST00000510833, ENST00000533201, ENST00000891922, ENST00000891923

RefSeq mRNA: 1 — MANE Select: NM_182628 NM_182628

CCDS: CCDS3037

Canonical transcript exons

ENST00000352312 — 17 exons

Exon	Start	End
ENSE00001079375	126416316	126416508
ENSE00001079376	126418611	126418774
ENSE00001079377	126418458	126418525
ENSE00001079378	126419076	126419156
ENSE00001079380	126419637	126419818
ENSE00001238754	126433069	126433204
ENSE00001238762	126423493	126423644
ENSE00001238772	126423325	126423376
ENSE00001238836	126414085	126414179
ENSE00001238846	126407172	126407252
ENSE00001238867	126436291	126436556
ENSE00003484118	126419980	126420021
ENSE00003548848	126395942	126396049
ENSE00003647871	126420103	126420229
ENSE00003657980	126434176	126434381
ENSE00003686724	126435559	126435652
ENSE00003842869	126394909	126394978

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 99.52.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8443 / max 112.8338, expressed in 152 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38347	0.7851	136
38346	0.0592	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.52	gold quality
right testis	UBERON:0004534	94.26	gold quality
left testis	UBERON:0004533	93.98	gold quality
bronchial epithelial cell	CL:0002328	93.65	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.61	gold quality
bronchus	UBERON:0002185	92.38	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.88	gold quality
testis	UBERON:0000473	90.24	gold quality
right lung	UBERON:0002167	85.72	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.99	gold quality
pancreatic ductal cell	CL:0002079	84.14	silver quality
nasal cavity epithelium	UBERON:0005384	83.88	gold quality
left uterine tube	UBERON:0001303	82.71	gold quality
fallopian tube	UBERON:0003889	81.99	gold quality
nasal cavity mucosa	UBERON:0001826	81.41	gold quality
mucosa of paranasal sinus	UBERON:0005030	80.29	gold quality
caudate nucleus	UBERON:0001873	80.22	gold quality
hypothalamus	UBERON:0001898	79.78	gold quality
nucleus accumbens	UBERON:0001882	79.56	gold quality
cortical plate	UBERON:0005343	77.56	gold quality
putamen	UBERON:0001874	73.22	gold quality
myocardium	UBERON:0002349	72.86	gold quality
oviduct epithelium	UBERON:0004804	72.54	gold quality
endocervix	UBERON:0000458	72.39	gold quality
amygdala	UBERON:0001876	71.43	gold quality
upper lobe of left lung	UBERON:0008952	70.45	gold quality
ventricular zone	UBERON:0003053	69.09	gold quality
upper lobe of lung	UBERON:0008948	69.09	gold quality
parotid gland	UBERON:0001831	68.91	gold quality
epithelium of nasopharynx	UBERON:0001951	68.81	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.71
E-GEOD-98556	no	28.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting CFAP100, 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-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-4768-3P	98.16	66.02	2330
HSA-MIR-506-5P	98.02	67.41	1065
HSA-MIR-3157-5P	97.41	67.61	998

Literature-anchored findings (GeneRIF, showing 1)

• We confirmed that the expression of CCDC37 in squamous cell carcinoma is regulated by DNA methylation of its specific promoter region. (PMID:22011669)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap100	ENSDARG00000111474
mus_musculus	Cfap100	ENSMUSG00000048794
rattus_norvegicus	Cfap100	ENSRNOG00000017959

Paralogs (3): CCDC42 (ENSG00000161973), CCDC38 (ENSG00000165972), CFAP73 (ENSG00000186710)

Protein

Protein identifiers

Cilia- and flagella-associated protein 100 — Q494V2 (reviewed: Q494V2)

Alternative names: Coiled-coil domain-containing protein 37

All UniProt accessions (2): E9PQV5, Q494V2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in ciliary/flagellar motility by regulating the assembly and the activity of axonemal inner dynein arm.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium axoneme.

Similarity. Belongs to the CFAP100 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q494V2-1	1	yes
Q494V2-2	2

RefSeq proteins (1): NP_872434* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025252	DUF4200	Domain
IPR051147	CFAP_domain-containing	Family

Pfam: PF13863

UniProt features (17 total): coiled-coil region 5, compositionally biased region 4, region of interest 3, sequence conflict 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q494V2-F1	74.85	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_INNER_DYNEIN_ARM_ASSEMBLY, GOBP_AXONEMAL_DYNEIN_COMPLEX_ASSEMBLY, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_ORGANELLE_ASSEMBLY, GOBP_MICROTUBULE_BUNDLE_FORMATION, chr3q21, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_AXONEME_ASSEMBLY, GOCC_CYTOPLASMIC_REGION, RYTGCNWTGGNR_UNKNOWN, GOCC_MOTILE_CILIUM, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY

GO Biological Process (2): cilium movement (GO:0003341), inner dynein arm assembly (GO:0036159)

GO Molecular Function (2): dynein complex binding (GO:0070840), protein binding (GO:0005515)

GO Cellular Component (7): motile cilium (GO:0031514), ciliary basal body (GO:0036064), axonemal doublet microtubule (GO:0097545), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cilium	2
microtubule-based movement	1
axonemal dynein complex assembly	1
protein-containing complex binding	1
binding	1
microtubule organizing center	1
axoneme	1
A axonemal microtubule	1
B axonemal microtubule	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

544 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP100	TMCC1	O94876	879
CFAP100	PODXL2	Q9NZ53	875
CFAP100	KLF15	Q9UIH9	861
CFAP100	PLXND1	Q9Y4D7	831
CFAP100	PLXNA1	Q9UIW2	688
CFAP100	CFAP73	A6NFT4	603
CFAP100	CCDC146	Q8IYE0	520
CFAP100	GATA2	P23769	520
CFAP100	CCDC42	Q96M95	518
CFAP100	CFAP119	A1A4V9	473
CFAP100	MARCHF10	Q8NA82	471
CFAP100	KCNK17	Q96T54	436
CFAP100	KIF24	Q5T7B8	412
CFAP100	ODAD1	Q96M63	398
CFAP100	CFAP184	Q2M329	391

IntAct

7 interactions, top by confidence:

A	B	Type	Score
CFAP100	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
SUV39H2	CFAP100	psi-mi:“MI:0915”(physical association)	0.370
SUV39H1	CFAP100	psi-mi:“MI:0915”(physical association)	0.370
KDM1A	CFAP100	psi-mi:“MI:0915”(physical association)	0.370
	CFAP100	psi-mi:“MI:0915”(physical association)	0.370
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (29): CCDC37 (Reconstituted Complex), SYCE1 (Two-hybrid), HIST1H2BH (Proximity Label-MS), CCDC37 (Two-hybrid), CCDC37 (Affinity Capture-RNA), CCDC37 (Affinity Capture-MS), CCDC37 (Affinity Capture-MS), COLEC12 (Cross-Linking-MS (XL-MS)), CCDC37 (Proximity Label-MS), CCDC37 (Proximity Label-MS), CCDC37 (Proximity Label-MS), CCDC37 (Proximity Label-MS), CCDC37 (Proximity Label-MS), CCDC37 (Proximity Label-MS), CCDC37 (Proximity Label-MS)

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: Q494V2, Q4R8V8, Q502W7, Q80VN0, Q8CDN8, Q95JL6, A8I4E9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	95
Likely benign	11
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2749 predictions. Top by Δscore:

Variant	Effect	Δscore
3:126396046:GACA:G	donor_gain	1.0000
3:126396050:G:GG	donor_gain	1.0000
3:126418609:A:AG	acceptor_gain	1.0000
3:126418610:G:GG	acceptor_gain	1.0000
3:126418610:GTAT:G	acceptor_gain	1.0000
3:126418730:G:GG	donor_gain	1.0000
3:126418739:G:GT	donor_gain	1.0000
3:126418754:C:G	donor_gain	1.0000
3:126418771:GAGC:G	donor_gain	1.0000
3:126418773:GC:G	donor_gain	1.0000
3:126418775:G:GG	donor_gain	1.0000
3:126419764:G:GT	donor_gain	1.0000
3:126420101:AGAGG:A	acceptor_gain	1.0000
3:126420102:GA:G	acceptor_gain	1.0000
3:126420102:GAGGG:G	acceptor_gain	1.0000
3:126420226:GAGG:G	donor_gain	1.0000
3:126420228:GG:G	donor_gain	1.0000
3:126420229:GG:G	donor_gain	1.0000
3:126423407:G:GT	donor_gain	1.0000
3:126423607:GAGC:G	donor_gain	1.0000
3:126423610:C:G	donor_gain	1.0000
3:126423641:GCAT:G	donor_gain	1.0000
3:126423645:G:GG	donor_gain	1.0000
3:126423646:T:G	donor_loss	1.0000
3:126433065:CCA:C	acceptor_loss	1.0000
3:126433067:A:AG	acceptor_gain	1.0000
3:126433067:AG:A	acceptor_gain	1.0000
3:126433067:AGG:A	acceptor_gain	1.0000
3:126433068:G:GA	acceptor_gain	1.0000
3:126433068:G:GC	acceptor_loss	1.0000

AlphaMissense

4055 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:126423508:T:C	F384L	0.990
3:126423510:C:A	F384L	0.990
3:126423510:C:G	F384L	0.990
3:126418731:T:C	F203L	0.989
3:126418733:C:A	F203L	0.989
3:126418733:C:G	F203L	0.989
3:126419077:G:C	A218P	0.988
3:126418764:G:C	A214P	0.987
3:126414114:T:C	F54L	0.985
3:126414116:C:A	F54L	0.985
3:126414116:C:G	F54L	0.985
3:126423509:T:C	F384S	0.985
3:126433089:T:C	L436P	0.983
3:126418506:G:C	R156P	0.981
3:126419693:T:C	L263P	0.981
3:126419129:T:C	L235P	0.979
3:126418689:G:C	A189P	0.977
3:126423527:T:C	L390P	0.977
3:126423563:T:C	L402P	0.976
3:126423569:T:C	L404P	0.974
3:126418722:T:C	F200L	0.973
3:126418724:C:A	F200L	0.973
3:126418724:C:G	F200L	0.973
3:126418648:T:C	L175P	0.970
3:126434303:T:C	L517P	0.970
3:126419702:T:C	L266P	0.969
3:126418514:T:C	F159L	0.968
3:126418516:C:A	F159L	0.968
3:126418516:C:G	F159L	0.968
3:126423548:T:C	L397P	0.967

dbSNP variants (sampled 300 via entrez): RS1000038244 (3:126430499 TAA>T), RS1000163692 (3:126424218 A>G), RS1000310973 (3:126396974 A>T), RS1000313787 (3:126435808 A>G), RS1000356812 (3:126408012 A>G), RS1000427921 (3:126401943 C>T), RS1000509803 (3:126423175 A>G), RS1000588553 (3:126435534 T>A,G), RS1000615846 (3:126417922 C>A), RS1000627331 (3:126413641 G>A), RS1000692975 (3:126400762 G>A), RS1000776549 (3:126430212 A>C,T), RS1000808101 (3:126407054 G>A), RS1000876329 (3:126406499 G>A), RS1000900342 (3:126434919 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
GSK-J4	decreases expression	1
bisphenol F	affects cotreatment, increases methylation	1
bisphenol A	affects cotreatment, decreases methylation	1
benzo(e)pyrene	increases methylation	1
CGP 52608	affects binding, increases reaction	1
Fulvestrant	decreases methylation, increases methylation, affects cotreatment	1
Air Pollutants	increases abundance, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Methapyrilene	increases methylation	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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