CFAP36

Summary

CFAP36 (cilia and flagella associated protein 36, HGNC:30540) is a protein-coding gene on chromosome 2p16.1, encoding Cilia- and flagella-associated protein 36 (Q96G28). May act as an effector for ARL3.

Located in ciliary transition zone.

Source: NCBI Gene 112942 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 65 total
• MANE Select transcript: NM_080667

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30540
Approved symbol	CFAP36
Name	cilia and flagella associated protein 36
Location	2p16.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC15407, BARTL1
Ensembl gene	ENSG00000163001
Ensembl biotype	protein_coding
Entrez	112942

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 15 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000339012, ENST00000349456, ENST00000403007, ENST00000406691, ENST00000407816, ENST00000481791, ENST00000490934, ENST00000904948, ENST00000904949, ENST00000904950, ENST00000904951, ENST00000904952, ENST00000924584, ENST00000924585, ENST00000959251, ENST00000959252, ENST00000959253

RefSeq mRNA: 2 — MANE Select: NM_080667 NM_001282761, NM_080667

CCDS: CCDS1854, CCDS62911

Canonical transcript exons

ENST00000349456 — 10 exons

Exon	Start	End
ENSE00001070505	55544220	55544369
ENSE00001070509	55528878	55528992
ENSE00001146757	55522102	55522166
ENSE00001739672	55523721	55523822
ENSE00001880981	55519718	55519916
ENSE00001913381	55544907	55545079
ENSE00003490464	55535712	55535763
ENSE00003578022	55543938	55544074
ENSE00003613074	55533873	55533960
ENSE00003670125	55537483	55537585

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 98.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 49.6260 / max 1062.1675, expressed in 1821 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20343	47.9097	1821
20342	1.7163	1078

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.67	gold quality
adenohypophysis	UBERON:0002196	98.60	gold quality
pituitary gland	UBERON:0000007	98.50	gold quality
right testis	UBERON:0004534	98.46	gold quality
right uterine tube	UBERON:0001302	97.81	gold quality
calcaneal tendon	UBERON:0003701	97.75	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.74	gold quality
nucleus accumbens	UBERON:0001882	97.69	gold quality
hypothalamus	UBERON:0001898	97.68	gold quality
right frontal lobe	UBERON:0002810	97.61	gold quality
anterior cingulate cortex	UBERON:0009835	97.52	gold quality
testis	UBERON:0000473	97.49	gold quality
caudate nucleus	UBERON:0001873	97.36	gold quality
putamen	UBERON:0001874	97.28	gold quality
islet of Langerhans	UBERON:0000006	97.27	gold quality
amygdala	UBERON:0001876	97.13	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.12	gold quality
prefrontal cortex	UBERON:0000451	96.99	gold quality
left ovary	UBERON:0002119	96.85	gold quality
left lobe of thyroid gland	UBERON:0001120	96.80	gold quality
pons	UBERON:0000988	96.79	gold quality
bronchial epithelial cell	CL:0002328	96.75	gold quality
right ovary	UBERON:0002118	96.59	gold quality
neocortex	UBERON:0001950	96.52	gold quality
thyroid gland	UBERON:0002046	96.51	gold quality
frontal cortex	UBERON:0001870	96.48	gold quality
bronchus	UBERON:0002185	96.42	gold quality
forebrain	UBERON:0001890	96.40	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.38	gold quality
right lobe of thyroid gland	UBERON:0001119	96.36	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	28.72
E-ANND-3	yes	11.81
E-MTAB-9388	yes	7.03
E-MTAB-10137	yes	4.11
E-CURD-112	no	2.84

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• The association between Yo and CCDC104 antibodies in paraneoplastic neurological syndromes may indicate functional similarities. (PMID:19680650)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap36	ENSDARG00000037079
mus_musculus	Cfap36	ENSMUSG00000020462
rattus_norvegicus	Cfap36	ENSRNOG00000003901
drosophila_melanogaster	CG14367	FBGN0038170
caenorhabditis_elegans		WBGENE00022435

Protein

Protein identifiers

Cilia- and flagella-associated protein 36 — Q96G28 (reviewed: Q96G28)

Alternative names: Coiled-coil domain-containing protein 104

All UniProt accessions (4): B5MC35, B5MCA1, B5MD16, Q96G28

UniProt curated annotations — full annotation on UniProt →

Function. May act as an effector for ARL3.

Subunit / interactions. Interacts with ARL3.

Subcellular location. Nucleus. Cytoplasm. Cell projection. Cilium. Flagellum.

Tissue specificity. Expressed in several human tissues including brain, testis, heart, lung, pancreas and spleen (at protein level).

Similarity. Belongs to the CFAP36 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96G28-1	1	yes
Q96G28-2	2

RefSeq proteins (2): NP_001269690, NP_542398* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR023379	BART_dom	Domain
IPR038888	CFAP36	Family
IPR042541	BART_sf	Homologous_superfamily

Pfam: PF11527

UniProt features (15 total): region of interest 3, modified residue 3, sequence variant 3, compositionally biased region 3, chain 1, splice variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96G28-F1	73.92	0.35

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 201, 85, 147

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): CCAWYNNGAAR_UNKNOWN, GOCC_CYTOPLASMIC_REGION, GOCC_MOTILE_CILIUM, GOCC_CILIARY_TRANSITION_ZONE, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GOCC_CILIARY_BASE, WGTTNNNNNAAA_UNKNOWN, GOCC_CILIUM, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, HAMAI_APOPTOSIS_VIA_TRAIL_UP, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, ZNF585B_TARGET_GENES, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2

GO Biological Process (0):

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

GO Cellular Component (8): nucleus (GO:0005634), axoneme (GO:0005930), motile cilium (GO:0031514), ciliary transition zone (GO:0035869), ciliary base (GO:0097546), cytoplasm (GO:0005737), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cilium	3
binding	1
intracellular membrane-bounded organelle	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
ciliary transition zone	1
ciliary transition fiber	1
intracellular anatomical structure	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

346 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP36	ARL3	P36405	754
CFAP36	FAM161B	Q96MY7	618
CFAP36	TTC29	Q8NA56	572
CFAP36	FAM81B	Q96LP2	533
CFAP36	CCDC63	Q8NA47	510
CFAP36	DNAAF9	Q5TEA3	480
CFAP36	RIBC2	Q9H4K1	460
CFAP36	CFAP184	Q2M329	453
CFAP36	SPICE1	Q8N0Z3	451
CFAP36	VWA1	Q6PCB0	451
CFAP36	UNC119B	A6NIH7	435
CFAP36	CDR2	Q01850	429
CFAP36	FOXB1	Q99853	411
CFAP36	TEKT3	Q9BXF9	404
CFAP36	ROPN1L	Q96C74	399

IntAct

20 interactions, top by confidence:

A	B	Type	Score
ARL3	UNC119B	psi-mi:“MI:0914”(association)	0.730
CFAP36	SNTB2	psi-mi:“MI:0914”(association)	0.620
CFAP36	SNTB2	psi-mi:“MI:0915”(physical association)	0.620
Arl3	CFAP36	psi-mi:“MI:0407”(direct interaction)	0.560
CFAP36	DAZAP2	psi-mi:“MI:0915”(physical association)	0.560
DAZAP2	CFAP36	psi-mi:“MI:0915”(physical association)	0.560
CFAP36	ARL2	psi-mi:“MI:0914”(association)	0.530
CFAP36	Arl2	psi-mi:“MI:0407”(direct interaction)	0.440
ARL3		psi-mi:“MI:0914”(association)	0.350
ARL2	PTPDC1	psi-mi:“MI:0914”(association)	0.350
ARL2	UNC119B	psi-mi:“MI:0914”(association)	0.350
NDN	HDLBP	psi-mi:“MI:2364”(proximity)	0.270
NDN	PABPC1	psi-mi:“MI:2364”(proximity)	0.270
RET	NUDT19	psi-mi:“MI:2364”(proximity)	0.270
FCHSD2	CFAP36	psi-mi:“MI:0915”(physical association)	0.000
	CFAP36	psi-mi:“MI:0915”(physical association)	0.000
CFAP36	RAC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (32): ARL2 (Affinity Capture-MS), OSBPL9 (Affinity Capture-MS), SNTB2 (Affinity Capture-MS), KCTD10 (Affinity Capture-MS), BDH2 (Affinity Capture-MS), CFAP36 (Reconstituted Complex), CFAP36 (Affinity Capture-MS), CFAP36 (Proximity Label-MS), CFAP36 (Proximity Label-MS), CFAP36 (Proximity Label-MS), CFAP36 (Proximity Label-MS), KCTD10 (Affinity Capture-MS), CFAP36 (Affinity Capture-MS), SNTB2 (Affinity Capture-MS), OSBPL9 (Affinity Capture-MS)

ESM2 similar proteins: A0A1S4D1D3, A0A1W2PR95, A1D9I5, A5D796, A7SD85, B0W6N3, D2K8N5, E1C760, E7EXT2, F7AEX0, O08836, O57476, P51951, P54729, P78318, P92948, Q0CU99, Q16543, Q16891, Q173M7, Q1DM35, Q2PIU8, Q2QY04, Q3ZC62, Q4V8E4, Q4W9M7, Q5AXH3, Q5EAC6, Q5M990, Q5PQS7, Q61081, Q61249, Q63692, Q6PID6, Q7SYB2, Q8C6E0, Q8CAQ8, Q8LDQ4, Q8R3N6, Q93VM9

Diamond homologs: Q1RM35, Q28IH8, Q3ZC62, Q4V8E4, Q7T0S7, Q8C6E0, Q95Y36, Q96G28, Q7SYL1, Q32PC9, Q4R930, Q4V8C5, Q5FW25, Q5R9K8, Q5ZKW5, Q6DDX7, Q9D385, Q9Y2Y0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	44
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1702 predictions. Top by Δscore:

Variant	Effect	Δscore
2:55519915:AGGTA:A	donor_loss	1.0000
2:55519916:GGT:G	donor_loss	1.0000
2:55519917:GTAAA:G	donor_loss	1.0000
2:55519918:T:A	donor_loss	1.0000
2:55522094:A:AG	acceptor_gain	1.0000
2:55522095:A:G	acceptor_gain	1.0000
2:55522097:T:G	acceptor_gain	1.0000
2:55522097:TTTAG:T	acceptor_loss	1.0000
2:55522098:TTAGT:T	acceptor_loss	1.0000
2:55522099:TAGTT:T	acceptor_loss	1.0000
2:55522100:A:AG	acceptor_gain	1.0000
2:55522100:A:C	acceptor_loss	1.0000
2:55522101:G:GG	acceptor_gain	1.0000
2:55522101:GT:G	acceptor_gain	1.0000
2:55522101:GTT:G	acceptor_gain	1.0000
2:55522101:GTTT:G	acceptor_gain	1.0000
2:55522101:GTTTT:G	acceptor_gain	1.0000
2:55522162:AACTA:A	donor_gain	1.0000
2:55522163:ACTA:A	donor_gain	1.0000
2:55522164:CTA:C	donor_gain	1.0000
2:55522164:CTAGT:C	donor_loss	1.0000
2:55522165:TA:T	donor_gain	1.0000
2:55522165:TAGTG:T	donor_loss	1.0000
2:55522166:AGT:A	donor_loss	1.0000
2:55522167:GTGA:G	donor_gain	1.0000
2:55522169:GAGTA:G	donor_loss	1.0000
2:55522171:G:GG	donor_gain	1.0000
2:55523715:TTTTA:T	acceptor_loss	1.0000
2:55523716:TTTA:T	acceptor_loss	1.0000
2:55523718:TA:T	acceptor_loss	1.0000

AlphaMissense

2278 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:55519874:T:A	W25R	0.999
2:55519874:T:C	W25R	0.999
2:55522104:T:C	F40L	0.999
2:55522106:T:A	F40L	0.999
2:55522106:T:G	F40L	0.999
2:55528920:T:C	F109L	0.999
2:55528922:T:A	F109L	0.999
2:55528922:T:G	F109L	0.999
2:55528960:T:C	L122P	0.999
2:55528965:G:C	A124P	0.999
2:55544983:T:A	L335H	0.999
2:55544983:T:C	L335P	0.999
2:55522105:T:C	F40S	0.998
2:55522146:C:G	H54D	0.998
2:55522155:T:G	Y57D	0.998
2:55523722:T:A	V61D	0.998
2:55523776:T:C	F79S	0.998
2:55528911:T:C	F106L	0.998
2:55528913:T:A	F106L	0.998
2:55528913:T:G	F106L	0.998
2:55528921:T:C	F109S	0.998
2:55519832:T:A	W11R	0.997
2:55519832:T:C	W11R	0.997
2:55519860:T:C	L20P	0.997
2:55519895:T:C	F32L	0.997
2:55519897:T:A	F32L	0.997
2:55519897:T:G	F32L	0.997
2:55522105:T:G	F40C	0.997
2:55522129:T:C	L48S	0.997
2:55522155:T:C	Y57H	0.997

dbSNP variants (sampled 300 via entrez): RS1000056935 (2:55536470 G>T), RS1000079986 (2:55521589 GTATA>G,GTA,GTATATA), RS1000121024 (2:55539042 T>C), RS1000149719 (2:55545236 T>C), RS1000174078 (2:55524884 G>A), RS1000347602 (2:55533316 G>A), RS1000430924 (2:55528234 T>C,G), RS1000432731 (2:55519509 C>T), RS1000500728 (2:55540858 C>T), RS1000587944 (2:55536501 A>G), RS1000676840 (2:55533098 C>T), RS1000682828 (2:55536771 G>A), RS1000737642 (2:55530170 A>C), RS1000742234 (2:55519235 G>C), RS1000906428 (2:55542619 C>T)

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

1 associations (top):

Study	Trait	p-value
GCST010002_365	Refractive error	3.000000e-34

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
sodium arsenite	increases abundance, increases expression	3
Cyclosporine	increases expression	3
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
K 7174	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Doxorubicin	increases expression	1
Ivermectin	decreases expression	1
Rotenone	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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