CFAP95

Summary

CFAP95 (cilia and flagella associated protein 95, HGNC:31422) is a protein-coding gene on chromosome 9q21.12, encoding Cilia- and flagella-associated protein 95 (Q5VTT2). 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 axonemal microtubule and plasma membrane.

Source: NCBI Gene 138255 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_001010940

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31422
Approved symbol	CFAP95
Name	cilia and flagella associated protein 95
Location	9q21.12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204711
Ensembl biotype	protein_coding
Entrez	138255

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000377197, ENST00000466872, ENST00000480564, ENST00000495399, ENST00000527647, ENST00000529131, ENST00000529446, ENST00000936456, ENST00000936457, ENST00000936458

RefSeq mRNA: 4 — MANE Select: NM_001010940 NM_001010940, NM_001308084, NM_001308085, NM_001308086

CCDS: CCDS35041, CCDS78403

Canonical transcript exons

ENST00000377197 — 6 exons

Exon	Start	End
ENSE00001473067	69905954	69906227
ENSE00001473072	69844517	69844625
ENSE00001473074	69820817	69821031
ENSE00003515718	69856555	69856673
ENSE00003528405	69886838	69886895
ENSE00003639731	69857909	69857977

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 99.28.

FANTOM5 (CAGE): breadth broad, TPM avg 2.5293 / max 151.9756, expressed in 287 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96847	1.6418	265
96848	0.8875	115

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	99.28	gold quality
bronchus	UBERON:0002185	98.82	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.84	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.04	gold quality
sperm	CL:0000019	92.87	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.60	gold quality
right uterine tube	UBERON:0001302	92.09	gold quality
nasal cavity epithelium	UBERON:0005384	90.14	gold quality
epithelium of nasopharynx	UBERON:0001951	89.26	gold quality
oviduct epithelium	UBERON:0004804	87.21	gold quality
pituitary gland	UBERON:0000007	85.47	gold quality
trachea	UBERON:0003126	84.41	gold quality
fallopian tube	UBERON:0003889	83.62	gold quality
left testis	UBERON:0004533	83.33	gold quality
right testis	UBERON:0004534	82.68	gold quality
adenohypophysis	UBERON:0002196	82.49	gold quality
testis	UBERON:0000473	81.84	gold quality
islet of Langerhans	UBERON:0000006	80.54	gold quality
nasal cavity mucosa	UBERON:0001826	80.39	gold quality
caput epididymis	UBERON:0004358	79.08	gold quality
body of tongue	UBERON:0011876	78.23	gold quality
secondary oocyte	CL:0000655	77.48	gold quality
adult organism	UBERON:0007023	76.93	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.96	gold quality
buccal mucosa cell	CL:0002336	73.56	silver quality
biceps brachii	UBERON:0001507	72.01	gold quality
right lung	UBERON:0002167	70.26	gold quality
tongue	UBERON:0001723	67.37	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	66.16	gold quality
endometrium	UBERON:0001295	65.27	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	61.83
E-HCAD-1	yes	26.59
E-MTAB-10287	yes	25.96
E-MTAB-9388	yes	11.40
E-MTAB-6524	no	70.50
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cfap95	ENSMUSG00000033053
rattus_norvegicus	Cfap95	ENSRNOG00000036615

Protein

Protein identifiers

Cilia- and flagella-associated protein 95 — Q5VTT2 (reviewed: Q5VTT2)

All UniProt accessions (4): E9PIA3, H0YD79, H0YDM9, Q5VTT2

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. Interacts with MYH9. Interacts with MYH10.

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

Tissue specificity. Expressed in undifferentiated embryonic stem cells. Expressed in airway epithelial cells.

Induction. Down-regulated following embryonic stem cells differentiation.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5VTT2-1	1	yes
Q5VTT2-2	2

RefSeq proteins (4): NP_001010940, NP_001295013, NP_001295014, NP_001295015 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027905	CFAP95	Family

Pfam: PF15139

UniProt features (7 total): topological domain 2, chain 1, transmembrane region 1, region of interest 1, glycosylation site 1, splice variant 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-Q5VTT2-F1	63.03	0.00

Functional residue map

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

Glycosylation sites (1): 75

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 54 (showing top): 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, chr9q21, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, RAO_BOUND_BY_SALL4_ISOFORM_B, 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 (0):

GO Cellular Component (10): cytoplasm (GO:0005737), axonemal microtubule (GO:0005879), plasma membrane (GO:0005886), sperm flagellum (GO:0036126), axonemal A tubule inner sheath (GO:0160111), cytoskeleton (GO:0005856), cilium (GO:0005929), membrane (GO:0016020), 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-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
intracellular anatomical structure	1
cytoplasmic microtubule	1
axoneme	1
membrane	1
cell periphery	1
9+2 motile cilium	1
A axonemal microtubule	1
axonemal microtubule doublet inner sheath	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

662 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP95	MORN5	Q5VZ52	639
CFAP95	ATP6V0D2	Q8N8Y2	498
CFAP95	FAM219A	Q8IW50	479
CFAP95	DPP6	P42658	463
CFAP95	DRICH1	Q6PGQ1	448
CFAP95	PPDPFL	Q8WWR9	413
CFAP95	TPRG1	Q6ZUI0	403
CFAP95	HDDC2	Q7Z4H3	400
CFAP95	PADI1	Q9ULC6	393
CFAP95	DPCD	Q9BVM2	378
CFAP95	FHIP2A	Q5W0V3	375
CFAP95	GPR176	Q14439	371
CFAP95	RSPH14	Q9UHP6	370
CFAP95	SHC2	P98077	361
CFAP95	ODF4	Q2M2E3	351

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CFAP95	PB2	psi-mi:“MI:0915”(physical association)	0.370
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GUX0, A0A3Q1MT14, A4D263, A6NL82, A6QQL5, A8QW39, B0UXH9, B5X5D0, B9EJX3, E1B9R1, F1MMV1, Q148A4, Q1JPL0, Q2T9T0, Q32KQ1, Q32L72, Q32L77, Q32P67, Q3V0J4, Q5BN46, Q5NC57, Q5NC83, Q5SPV6, Q5SS90, Q5SVJ3, Q5VTT2, Q5VZQ5, Q66HC0, Q66HR9, Q6AYM0, Q6NXP0, Q6P3G4, Q6ZVS7, Q80X60, Q8CDT5, Q8CDU5, Q8N5S3, Q8N7U6, Q8N865

Diamond homologs: Q32L77, Q5VTT2, Q9CQC3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	1
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1258 predictions. Top by Δscore:

Variant	Effect	Δscore
9:69844515:A:G	acceptor_gain	1.0000
9:69844622:CCCA:C	donor_gain	1.0000
9:69844623:CCA:C	donor_gain	1.0000
9:69844626:G:GG	donor_gain	1.0000
9:69857978:G:GG	donor_gain	1.0000
9:69886896:G:GG	donor_gain	1.0000
9:69821029:CTGGT:C	donor_loss	0.9900
9:69821030:TGGT:T	donor_loss	0.9900
9:69821031:GGT:G	donor_loss	0.9900
9:69821032:G:GC	donor_loss	0.9900
9:69821032:G:GG	donor_gain	0.9900
9:69821033:T:G	donor_loss	0.9900
9:69821034:G:GT	donor_loss	0.9900
9:69826507:G:GG	donor_gain	0.9900
9:69844516:G:A	acceptor_gain	0.9900
9:69844516:G:GG	acceptor_gain	0.9900
9:69844621:CCCCA:C	donor_gain	0.9900
9:69844624:CA:C	donor_gain	0.9900
9:69844624:CAGT:C	donor_loss	0.9900
9:69844625:AG:A	donor_loss	0.9900
9:69844626:GTAAG:G	donor_loss	0.9900
9:69844627:T:TG	donor_loss	0.9900
9:69844628:AAG:A	donor_loss	0.9900
9:69844629:A:AA	donor_loss	0.9900
9:69844630:G:C	donor_loss	0.9900
9:69856553:A:AG	acceptor_gain	0.9900
9:69856554:G:GG	acceptor_gain	0.9900
9:69886892:ACATG:A	donor_loss	0.9900
9:69886893:CATG:C	donor_loss	0.9900
9:69886894:ATG:A	donor_loss	0.9900

AlphaMissense

1502 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:69906008:T:C	F188L	0.969
9:69906010:C:A	F188L	0.969
9:69906010:C:G	F188L	0.969
9:69906050:T:A	W202R	0.935
9:69906050:T:C	W202R	0.935
9:69906009:T:C	F188S	0.907
9:69905992:A:C	R182S	0.894
9:69905992:A:T	R182S	0.894
9:69906062:A:C	S206R	0.891
9:69906064:T:A	S206R	0.891
9:69906064:T:G	S206R	0.891
9:69821003:T:C	Y42H	0.872
9:69906052:G:C	W202C	0.869
9:69906052:G:T	W202C	0.869
9:69821030:T:A	W51R	0.868
9:69821030:T:C	W51R	0.868
9:69857934:T:C	F136L	0.867
9:69857936:T:A	F136L	0.867
9:69857936:T:G	F136L	0.867
9:69820970:G:C	G31R	0.866
9:69906009:T:G	F188C	0.866
9:69844517:G:C	W51C	0.857
9:69844517:G:T	W51C	0.857
9:69906079:T:A	N211K	0.853
9:69906079:T:G	N211K	0.853
9:69844536:T:C	F58L	0.844
9:69844538:T:A	F58L	0.844
9:69844538:T:G	F58L	0.844
9:69906002:T:C	S186P	0.839
9:69821004:A:C	Y42S	0.838

dbSNP variants (sampled 300 via entrez): RS1000002953 (9:69878159 G>A,C), RS1000050827 (9:69848999 A>G), RS1000063429 (9:69865053 A>G), RS1000121265 (9:69902101 C>T), RS1000140779 (9:69823494 C>T), RS1000156208 (9:69829929 C>T), RS1000172231 (9:69823640 G>A), RS1000220693 (9:69828540 G>A), RS1000268387 (9:69820512 G>GGGGT), RS1000270929 (9:69861057 T>C), RS1000360488 (9:69861004 G>A), RS1000397191 (9:69896146 G>A), RS1000406155 (9:69820184 C>T), RS1000436188 (9:69903110 T>C), RS1000444740 (9:69829549 A>G)

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

5 associations (top):

Study	Trait	p-value
GCST005580_253	Intraocular pressure	2.000000e-10
GCST005580_71	Intraocular pressure	1.000000e-11
GCST009208_5	Transverse temporal cortex volume	4.000000e-06
GCST009310_27	Sensorimotor dexterity	4.000000e-08
GCST011176_10	Stroke	2.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement
EFO:0008354	cognitive function measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, affects cotreatment	8
entinostat	increases expression, affects cotreatment	2
methylmercuric chloride	decreases expression	1
trichostatin A	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
Decitabine	affects expression	1
Vorinostat	increases expression, affects cotreatment	1
Panobinostat	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects expression	1
Smoke	increases abundance, increases expression	1

Clinical trials (associated diseases)

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