CFAP96

Summary

CFAP96 (cilia and flagella associated protein 96, HGNC:34346) is a protein-coding gene on chromosome 4q35.1, encoding Cilia-and flagella-associated protein 96 (A7E2U8).

Located in 9+0 non-motile cilium; centrosome; and cytoplasmic microtubule.

Source: NCBI Gene 441054 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 71 total — 1 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_001114357

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34346
Approved symbol	CFAP96
Name	cilia and flagella associated protein 96
Location	4q35.1
Locus type	gene with protein product
Status	Approved
Aliases	LOC441054
Ensembl gene	ENSG00000205129
Ensembl biotype	protein_coding
Entrez	441054

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 nonsense_mediated_decay

ENST00000378850, ENST00000508698, ENST00000511138, ENST00000511581, ENST00000931375, ENST00000931376, ENST00000931377, ENST00000931378, ENST00000931379, ENST00000931380, ENST00000944291

RefSeq mRNA: 2 — MANE Select: NM_001114357 NM_001114357, NM_001346007

CCDS: CCDS47169

Canonical transcript exons

ENST00000378850 — 8 exons

Exon	Start	End
ENSE00001479018	185431982	185432201
ENSE00002026396	185429334	185429511
ENSE00002044463	185449596	185449826
ENSE00003516402	185444964	185445130
ENSE00003530865	185436046	185436183
ENSE00003667510	185440540	185440719
ENSE00003787993	185436284	185436359
ENSE00003916340	185426254	185426396

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 98.72.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9552 / max 48.7172, expressed in 668 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
50883	1.9552	668

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.72	gold quality
right uterine tube	UBERON:0001302	97.58	gold quality
bronchial epithelial cell	CL:0002328	97.27	gold quality
secondary oocyte	CL:0000655	96.96	gold quality
bronchus	UBERON:0002185	95.59	gold quality
oviduct epithelium	UBERON:0004804	93.32	gold quality
sperm	CL:0000019	93.04	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.33	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.90	gold quality
fallopian tube	UBERON:0003889	85.76	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.64	gold quality
caput epididymis	UBERON:0004358	84.23	gold quality
left testis	UBERON:0004533	84.12	gold quality
nasal cavity epithelium	UBERON:0005384	83.40	silver quality
right testis	UBERON:0004534	83.19	gold quality
testis	UBERON:0000473	82.90	gold quality
epithelium of nasopharynx	UBERON:0001951	82.63	gold quality
caudate nucleus	UBERON:0001873	79.77	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.76	gold quality
nucleus accumbens	UBERON:0001882	77.71	gold quality
endothelial cell	CL:0000115	77.30	gold quality
thyroid gland	UBERON:0002046	77.07	gold quality
left lobe of thyroid gland	UBERON:0001120	76.92	gold quality
putamen	UBERON:0001874	76.72	gold quality
right lobe of thyroid gland	UBERON:0001119	76.57	gold quality
adenohypophysis	UBERON:0002196	76.50	gold quality
pituitary gland	UBERON:0000007	75.44	gold quality
adult organism	UBERON:0007023	73.24	gold quality
nasal cavity mucosa	UBERON:0001826	72.69	gold quality
hypothalamus	UBERON:0001898	72.41	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.40
E-MTAB-9388	yes	8.07

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• C4orf47 Contributes to the Induction of Stem-like Properties in Gallbladder Cancer Under Hypoxia. (PMID:37097647)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap96	ENSDARG00000037142
mus_musculus	Cfap96	ENSMUSG00000071103
rattus_norvegicus	Cfap96	ENSRNOG00000038819

Protein

Protein identifiers

Cilia-and flagella-associated protein 96 — A7E2U8 (reviewed: A7E2U8)

All UniProt accessions (4): A7E2U8, D6R9T4, D6RB10, D6RCA9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Tissue specificity. Detected in testis and fetal liver.

Similarity. Belongs to the CFAP96 family.

RefSeq proteins (2): NP_001107829, NP_001332936 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029358	CFAP96	Family

Pfam: PF15239

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A7E2U8-F1	74.34	0.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOCC_CENTROSOME, chr4q35, HOOI_ST7_TARGETS_DN, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEN_METABOLIC_SYNDROM_NETWORK, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, GOCC_NON_MOTILE_CILIUM, GOCC_9PLUS0_NON_MOTILE_CILIUM, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (5): centrosome (GO:0005813), cytoplasmic microtubule (GO:0005881), 9+0 non-motile cilium (GO:0097731), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
centriole	1
microtubule organizing center	1
cytoplasm	1
microtubule	1
non-motile cilium	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

372 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP96	CFAP184	Q2M329	772
CFAP96	SPMIP4	Q8N865	668
CFAP96	CFAP90	A4QMS7	642
CFAP96	CFAP299	Q6V702	618
CFAP96	IQUB	Q8NA54	607
CFAP96	CLXN	Q9HAE3	595
CFAP96	PIERCE1	Q5BN46	593
CFAP96	CCDC116	Q8IYX3	580
CFAP96	CCDC38	Q502W7	580
CFAP96	ARMC3	Q5W041	545
CFAP96	CFAP263	Q9H0I3	527
CFAP96	CCDC146	Q8IYE0	523
CFAP96	RIMKLA	Q8IXN7	522
CFAP96	CFAP97	Q9P2B7	518
CFAP96	ZNF728	P0DKX0	503

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CFAP96	NPM1	psi-mi:“MI:0915”(physical association)	0.400
CFAP96	USP9Y	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (3): NPM1 (Proximity Label-MS), USP9Y (Affinity Capture-MS), NPM1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GUX0, A0A3Q1MT14, A1A5R9, A2AVQ5, A4D263, A7E2U8, B1H283, B5X5D0, B9EJX3, F1MMV1, Q0P4C5, Q148A4, Q1LVQ2, Q2T9M0, Q2T9T0, Q32L72, Q32L77, Q3U1D9, Q3ZCV2, Q5NC83, Q5RBY8, Q5SPV6, Q5SS90, Q5SVJ3, Q5U228, Q5VTT2, Q5VZQ5, Q5XHC1, Q5XHX8, Q66HR9, Q6AYM0, Q6NU22, Q6NU51, Q6ZN28, Q7Z5V6, Q810P2, Q8AXQ3, Q8C8J0, Q8CDT5

Diamond homologs: A7E2U8, Q0P4C5, Q2T9M0, Q3U1D9, Q5XHC1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	44
Likely benign	5
Benign	5

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
2663881	NM_018359.5(UFSP2):c.110_111del (p.His37fs)	Pathogenic
3340501	NM_018359.5(UFSP2):c.623del (p.Asn208fs)	Likely pathogenic

SpliceAI

1057 predictions. Top by Δscore:

Variant	Effect	Δscore
4:185429507:TAATC:T	donor_gain	1.0000
4:185429509:ATC:A	donor_gain	1.0000
4:185429509:ATCGT:A	donor_loss	1.0000
4:185429510:TCGTA:T	donor_loss	1.0000
4:185429512:G:C	donor_loss	1.0000
4:185429512:G:GG	donor_gain	1.0000
4:185429513:T:A	donor_loss	1.0000
4:185432202:G:GG	donor_gain	1.0000
4:185436021:A:AG	acceptor_gain	1.0000
4:185440531:A:AG	acceptor_gain	1.0000
4:185440532:A:G	acceptor_gain	1.0000
4:185440535:CACA:C	acceptor_loss	1.0000
4:185440537:CA:C	acceptor_loss	1.0000
4:185440538:A:AG	acceptor_gain	1.0000
4:185440539:G:GT	acceptor_gain	1.0000
4:185440539:GA:G	acceptor_gain	1.0000
4:185440539:GAA:G	acceptor_gain	1.0000
4:185440539:GAAA:G	acceptor_gain	1.0000
4:185440717:AAG:A	donor_gain	1.0000
4:185440717:AAGGT:A	donor_loss	1.0000
4:185440718:AG:A	donor_gain	1.0000
4:185440719:GG:G	donor_gain	1.0000
4:185440719:GGT:G	donor_loss	1.0000
4:185440720:G:GC	donor_loss	1.0000
4:185440720:G:GG	donor_gain	1.0000
4:185440721:T:A	donor_loss	1.0000
4:185445100:TTGA:T	donor_gain	1.0000
4:185445103:A:T	donor_gain	1.0000
4:185429488:A:AG	donor_gain	0.9900
4:185429508:AATC:A	donor_gain	0.9900

AlphaMissense

2030 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:185429457:T:C	F16L	0.989
4:185429459:T:A	F16L	0.989
4:185429459:T:G	F16L	0.989
4:185445105:A:C	S286R	0.989
4:185445107:T:A	S286R	0.989
4:185445107:T:G	S286R	0.989
4:185429458:T:C	F16S	0.979
4:185440612:T:C	F203L	0.977
4:185440614:T:A	F203L	0.977
4:185440614:T:G	F203L	0.977
4:185429447:G:C	R12S	0.971
4:185429447:G:T	R12S	0.971
4:185432173:T:C	F98L	0.970
4:185432175:C:A	F98L	0.970
4:185432175:C:G	F98L	0.970
4:185436170:G:A	G149R	0.970
4:185436170:G:C	G149R	0.970
4:185432065:T:C	F62L	0.966
4:185432067:T:A	F62L	0.966
4:185432067:T:G	F62L	0.966
4:185436059:A:C	S112R	0.966
4:185436061:C:A	S112R	0.966
4:185436061:C:G	S112R	0.966
4:185445066:T:C	F273L	0.963
4:185445068:C:A	F273L	0.963
4:185445068:C:G	F273L	0.963
4:185436183:G:A	G153D	0.962
4:185429452:G:A	G14D	0.958
4:185436177:G:A	G151E	0.958
4:185440582:T:C	F193L	0.956

dbSNP variants (sampled 300 via entrez): RS1000009846 (4:185418288 C>T), RS10000869 (4:185418295 A>G), RS1000093655 (4:185406912 C>A), RS1000106455 (4:185411482 T>G), RS1000138617 (4:185434523 A>G), RS10002982 (4:185422228 T>C), RS10003160 (4:185418430 A>C,G,T), RS1000368486 (4:185431769 C>T), RS1000440864 (4:185437795 T>G), RS1000470133 (4:185425115 T>A,C), RS1000521262 (4:185437586 G>C), RS1000586835 (4:185445918 C>T), RS1000644291 (4:185437510 A>G), RS1000673042 (4:185432789 G>A), RS1000694847 (4:185418095 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:142669, MIM:617974, MIM:620028

GenCC curated gene-disease

Mondo (3): hip dysplasia, Beukes type (MONDO:0007726), spondyloepimetaphyseal dysplasia, di rocco type (MONDO:0060702), developmental and epileptic encephalopathy 106 (MONDO:0031052)

Orphanet (1): Hip dysplasia, Beukes type (Orphanet:2114)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C564185	Hip Dysplasia, Beukes Type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

35 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases expression	3
methylmercuric chloride	decreases expression, increases expression	2
mercuric bromide	affects cotreatment, decreases expression	2
Oxygen	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
sotorasib	affects cotreatment, decreases expression	1
aminomethylphosphonic acid (AMPA)	increases expression	1
trichostatin A	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
jinfukang	increases expression, affects cotreatment	1
trametinib	affects cotreatment, decreases expression	1
PCI 5002	increases expression, affects cotreatment	1
NVP-BKM120	affects cotreatment, decreases expression	1
Vorinostat	decreases expression	1
Glyphosate	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Carbamazepine	affects expression	1
Cisplatin	affects cotreatment, increases expression	1
Demecolcine	increases expression	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Lipopolysaccharides	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Smoke	increases abundance, increases expression	1
T-2 Toxin	increases expression	1
Thimerosal	decreases expression	1

Clinical trials (associated diseases)

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