CFAP119

Summary

CFAP119 (cilia and flagella associated protein 119, HGNC:28078) is a protein-coding gene on chromosome 16p11.2, encoding Cilia- and flagella-associated protein 119 (A1A4V9).

Predicted to act upstream of or within gene expression; single fertilization; and sperm flagellum assembly. Predicted to be located in acrosomal vesicle and sperm principal piece. Predicted to be part of radial spoke. Predicted to be active in axoneme.

Source: NCBI Gene 90835 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 90 total
• MANE Select transcript: NM_001014979

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28078
Approved symbol	CFAP119
Name	cilia and flagella associated protein 119
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC104706
Ensembl gene	ENSG00000196118
Ensembl biotype	protein_coding
OMIM	618318
Entrez	90835

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 10 protein_coding, 6 retained_intron, 1 nonsense_mediated_decay

ENST00000433909, ENST00000535476, ENST00000537986, ENST00000541260, ENST00000543128, ENST00000543610, ENST00000544487, ENST00000544613, ENST00000544643, ENST00000545809, ENST00000545825, ENST00000546006, ENST00000892303, ENST00000892304, ENST00000892305, ENST00000892306, ENST00000957788

RefSeq mRNA: 2 — MANE Select: NM_001014979 NM_001014979, NM_001195620

CCDS: CCDS32434, CCDS55993

Canonical transcript exons

ENST00000543610 — 9 exons

Exon	Start	End
ENSE00002275386	30761545	30762062
ENSE00003461330	30759012	30759101
ENSE00003468137	30760606	30760668
ENSE00003469179	30759654	30759724
ENSE00003509236	30760284	30760453
ENSE00003539414	30759178	30759247
ENSE00003559032	30761198	30761229
ENSE00003568724	30759342	30759458
ENSE00003841363	30757423	30757654

Expression profiles

Bgee: expression breadth ubiquitous, 184 present calls, max score 96.80.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.7017 / max 50.8547, expressed in 1203 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157088	2.4409	1128
157089	0.1612	69
157090	0.0996	34

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	96.80	gold quality
bronchial epithelial cell	CL:0002328	93.93	gold quality
bronchus	UBERON:0002185	93.36	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.05	gold quality
left testis	UBERON:0004533	92.03	gold quality
right testis	UBERON:0004534	91.92	gold quality
adenohypophysis	UBERON:0002196	90.68	gold quality
sperm	CL:0000019	90.32	gold quality
pituitary gland	UBERON:0000007	89.67	gold quality
testis	UBERON:0000473	89.33	gold quality
nasal cavity epithelium	UBERON:0005384	86.79	silver quality
mucosa of paranasal sinus	UBERON:0005030	86.53	gold quality
cerebellar vermis	UBERON:0004720	85.83	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.59	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.44	gold quality
substantia nigra pars compacta	UBERON:0001965	84.94	gold quality
vena cava	UBERON:0004087	84.81	gold quality
hypothalamus	UBERON:0001898	84.77	gold quality
left lobe of thyroid gland	UBERON:0001120	83.41	gold quality
left ventricle myocardium	UBERON:0006566	83.29	gold quality
right lobe of thyroid gland	UBERON:0001119	83.08	gold quality
substantia nigra	UBERON:0002038	82.83	gold quality
cardiac muscle of right atrium	UBERON:0003379	82.63	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	82.59	gold quality
substantia nigra pars reticulata	UBERON:0001966	82.49	gold quality
midbrain	UBERON:0001891	82.44	gold quality
thyroid gland	UBERON:0002046	81.90	gold quality
right adrenal gland cortex	UBERON:0035827	81.70	gold quality
superior vestibular nucleus	UBERON:0007227	81.63	silver quality
metanephros cortex	UBERON:0010533	81.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.98
E-HCAD-13	no	2.97

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap119	ENSDARG00000096777
mus_musculus	Cfap119	ENSMUSG00000057176
rattus_norvegicus	Cfap119	ENSRNOG00000053015

Paralogs (1): C8orf74 (ENSG00000171060)

Protein

Protein identifiers

Cilia- and flagella-associated protein 119 — A1A4V9 (reviewed: A1A4V9)

Alternative names: Coiled-coil domain-containing protein 189

All UniProt accessions (5): A1A4V9, F5H7A8, H0YGC5, H3BNW1, H3BTQ9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell projection. Cilium. Flagellum. Cytoplasmic vesicle. Secretory vesicle. Acrosome. Cytoplasm.

Isoforms (4)

UniProt ID	Names	Canonical?
A1A4V9-1	1	yes
A1A4V9-2	2
A1A4V9-3	3
A1A4V9-4	4

RefSeq proteins (2): NP_001014979, NP_001182549 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032727	CLAMP	Family

Pfam: PF14769

UniProt features (10 total): splice variant 4, region of interest 2, chain 1, coiled-coil region 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A1A4V9-F1	74.17	0.48

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 (1): 34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): GOBP_SINGLE_FERTILIZATION, GOCC_SECRETORY_GRANULE, GOBP_MALE_GAMETE_GENERATION, GOBP_CILIUM_ORGANIZATION, chr16p11, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MOTILE_CILIUM_ASSEMBLY, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_FERTILIZATION, GOCC_CYTOPLASMIC_REGION, GOCC_SECRETORY_VESICLE

GO Biological Process (3): single fertilization (GO:0007338), gene expression (GO:0010467), sperm flagellum assembly (GO:0120316)

GO Molecular Function (0):

GO Cellular Component (9): radial spoke (GO:0001534), acrosomal vesicle (GO:0001669), cytoplasm (GO:0005737), sperm principal piece (GO:0097228), cilium (GO:0005929), axoneme (GO:0005930), cytoplasmic vesicle (GO:0031410), 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
fertilization	1
macromolecule biosynthetic process	1
developmental process involved in reproduction	1
spermatid development	1
flagellated sperm motility	1
motile cilium assembly	1
axoneme	1
protein-containing complex	1
secretory granule	1
intracellular anatomical structure	1
sperm flagellum	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
cytoplasm	1
intracellular vesicle	1
cilium	1

Protein interactions and networks

STRING

877 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP119	TMEM95	Q3KNT9	707
CFAP119	ARMC3	Q5W041	617
CFAP119	PDZD9	Q8IXQ8	598
CFAP119	PRSS36	Q5K4E3	571
CFAP119	TMEM139	Q8IV31	480
CFAP119	PRSS53	Q2L4Q9	477
CFAP119	CFAP100	Q494V2	473
CFAP119	DPY30	Q9C005	463
CFAP119	LRRIQ4	A6NIV6	445
CFAP119	MARCHF10	Q8NA82	441
CFAP119	TMED6	Q8WW62	433
CFAP119	KCNK17	Q96T54	430
CFAP119	SPAG17	Q6Q759	391
CFAP119	RABEP2	Q9H5N1	389
CFAP119	SLC26A8	Q96RN1	382

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CFAP119	SCGB1D2	psi-mi:“MI:0915”(physical association)	0.400
CFAP119	TUBA1A	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (4): C16orf93 (Affinity Capture-RNA), SCGB1D2 (Affinity Capture-MS), TUBA1A (Affinity Capture-MS), C16orf93 (Affinity Capture-MS)

ESM2 similar proteins: A1A4V9, A2A8U2, A4IFI1, A8E4X8, B0BMZ6, F1R7R1, G5E8P0, O75161, P12755, P59017, P59240, P85299, P97432, Q14DQ1, Q2HJA5, Q3B7M3, Q3U0L2, Q3ZBK7, Q3ZK22, Q53GS7, Q569K6, Q58DT5, Q5FVG6, Q5RAS2, Q5SNT2, Q5T7N3, Q5XI52, Q60698, Q6NZQ0, Q80U62, Q812A5, Q8C0R7, Q8C190, Q8CC12, Q8IWY9, Q8IYY4, Q8N9B5, Q8NFW9, Q8R1F1, Q8R322

Diamond homologs: A1A4V9, B0BMZ6, Q6NZQ0, Q6P047

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	57
Likely benign	13
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1618 predictions. Top by Δscore:

Variant	Effect	Δscore
16:30757650:GTGGC:G	acceptor_gain	1.0000
16:30757652:GGC:G	acceptor_gain	1.0000
16:30757653:GC:G	acceptor_gain	1.0000
16:30757654:CC:C	acceptor_gain	1.0000
16:30757655:C:CA	acceptor_loss	1.0000
16:30757655:C:CC	acceptor_gain	1.0000
16:30757664:C:CT	acceptor_gain	1.0000
16:30757665:A:T	acceptor_gain	1.0000
16:30759010:A:AC	donor_gain	1.0000
16:30759011:C:CC	donor_gain	1.0000
16:30759011:CTTGG:C	donor_gain	1.0000
16:30759457:CG:C	acceptor_gain	1.0000
16:30759459:C:CC	acceptor_gain	1.0000
16:30760304:T:TA	donor_gain	1.0000
16:30760450:CACC:C	acceptor_gain	1.0000
16:30760451:ACC:A	acceptor_gain	1.0000
16:30760452:CC:C	acceptor_gain	1.0000
16:30760452:CCCT:C	acceptor_gain	1.0000
16:30760453:CC:C	acceptor_gain	1.0000
16:30760454:C:CA	acceptor_loss	1.0000
16:30760454:C:CC	acceptor_gain	1.0000
16:30760454:C:T	acceptor_gain	1.0000
16:30760455:T:C	acceptor_gain	1.0000
16:30760455:T:TC	acceptor_gain	1.0000
16:30760604:A:AC	donor_gain	1.0000
16:30760604:ACTC:A	donor_gain	1.0000
16:30760605:C:CC	donor_gain	1.0000
16:30760605:CTCC:C	donor_gain	1.0000
16:30760607:C:CA	donor_gain	1.0000
16:30760618:G:C	donor_gain	1.0000

AlphaMissense

2155 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:30760301:A:G	L151P	0.987
16:30759433:A:G	F189S	0.986
16:30761199:A:G	W79R	0.985
16:30761199:A:T	W79R	0.985
16:30759379:C:G	R207P	0.984
16:30759386:A:C	Y205D	0.983
16:30760668:C:A	W79C	0.983
16:30760668:C:G	W79C	0.983
16:30759351:G:C	F216L	0.981
16:30759351:G:T	F216L	0.981
16:30759353:A:G	F216L	0.981
16:30760385:A:G	L123P	0.980
16:30759447:G:C	F184L	0.979
16:30759447:G:T	F184L	0.979
16:30759449:A:G	F184L	0.979
16:30759457:C:G	R181P	0.977
16:30759365:A:C	Y212D	0.975
16:30759382:A:G	F206S	0.975
16:30759444:G:C	S185R	0.974
16:30759444:G:T	S185R	0.974
16:30759446:T:G	S185R	0.974
16:30759360:T:A	K213N	0.973
16:30759360:T:G	K213N	0.973
16:30760362:A:G	C131R	0.973
16:30760363:G:C	F130L	0.973
16:30760363:G:T	F130L	0.973
16:30760365:A:G	F130L	0.973
16:30760320:A:G	C145R	0.972
16:30759696:G:C	C166W	0.971
16:30760346:A:G	F136S	0.971

dbSNP variants (sampled 300 via entrez): RS1000558135 (16:30761969 G>C), RS1000992488 (16:30762209 A>C,G,T), RS1001075788 (16:30761500 C>G,T), RS1001191906 (16:30760863 A>C,G), RS1002247475 (16:30761764 T>C,G), RS1002584684 (16:30759380 G>A), RS1002601654 (16:30762019 T>C), RS1003197851 (16:30762935 C>T), RS1003387879 (16:30757525 T>C), RS1003391873 (16:30763563 G>A,C), RS1003422986 (16:30763817 G>A), RS1004041986 (16:30762053 T>C), RS1004531229 (16:30758068 TTC>T), RS1004611577 (16:30763875 C>T), RS1004790704 (16:30758505 T>A)

Disease associations

OMIM: gene MIM:618318 | disease phenotypes: MIM:616172

GenCC curated gene-disease

Mondo (1): generalized epilepsy with febrile seizures plus, type 9 (MONDO:0014517)

Orphanet (1): Genetic epilepsy with febrile seizure plus (Orphanet:36387)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006952_9	Feeling tense	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009596	feeling tense measurement

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
Tobacco Smoke Pollution	decreases expression	2
bisphenol A	affects cotreatment, decreases methylation	1
sodium arsenite	increases abundance, increases expression	1
nickel sulfate	increases expression	1
belinostat	increases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Rotenone	decreases expression	1
Smoke	increases abundance, increases expression	1
Valproic Acid	decreases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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