CFAP97

Summary

CFAP97 (cilia and flagella associated protein 97, HGNC:29276) is a protein-coding gene on chromosome 4q35.1, encoding Cilia- and flagella-associated protein 97 (Q9P2B7).

At a glance

• Clinical variants (ClinVar): 128 total — 2 pathogenic
• MANE Select transcript: NM_020827

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29276
Approved symbol	CFAP97
Name	cilia and flagella associated protein 97
Location	4q35.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434F1728, hmw
Ensembl gene	ENSG00000164323
Ensembl biotype	protein_coding
OMIM	616047
Entrez	57587

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 14 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000458385, ENST00000502992, ENST00000503223, ENST00000514798, ENST00000647728, ENST00000873856, ENST00000927457, ENST00000927458, ENST00000927459, ENST00000927460, ENST00000927461, ENST00000927462, ENST00000927463, ENST00000968391, ENST00000968392

RefSeq mRNA: 2 — MANE Select: NM_020827 NM_001292033, NM_020827

CCDS: CCDS47168, CCDS75216

Canonical transcript exons

ENST00000458385 — 5 exons

Exon	Start	End
ENSE00001083483	185175786	185176051
ENSE00001309457	185190143	185191212
ENSE00001727232	185164029	185164179
ENSE00001759082	185159665	185162925
ENSE00002061385	185203898	185204000

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 98.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.6277 / max 265.9175, expressed in 1776 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
55246	18.4211	1765
55247	0.8551	519
55241	0.1701	21
55242	0.1198	25
55244	0.0356	8
55245	0.0131	4
55243	0.0058	3
203449	0.0045	3
203450	0.0026	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	98.14	gold quality
epithelial cell of pancreas	CL:0000083	97.74	gold quality
oviduct epithelium	UBERON:0004804	97.33	gold quality
pigmented layer of retina	UBERON:0001782	97.21	gold quality
retina	UBERON:0000966	97.18	gold quality
germinal epithelium of ovary	UBERON:0001304	96.76	gold quality
upper arm skin	UBERON:0004263	96.52	gold quality
caput epididymis	UBERON:0004358	96.44	gold quality
cauda epididymis	UBERON:0004360	96.35	gold quality
skin of hip	UBERON:0001554	96.20	gold quality
parietal pleura	UBERON:0002400	96.17	gold quality
calcaneal tendon	UBERON:0003701	96.02	gold quality
sperm	CL:0000019	95.98	gold quality
tibia	UBERON:0000979	95.93	gold quality
kidney epithelium	UBERON:0004819	95.93	gold quality
epithelium of mammary gland	UBERON:0003244	95.74	gold quality
mammary duct	UBERON:0001765	95.71	gold quality
visceral pleura	UBERON:0002401	95.57	gold quality
cartilage tissue	UBERON:0002418	95.25	gold quality
upper leg skin	UBERON:0004262	95.19	gold quality
corpus epididymis	UBERON:0004359	95.17	gold quality
layer of synovial tissue	UBERON:0007616	95.15	gold quality
saphenous vein	UBERON:0007318	94.91	gold quality
seminal vesicle	UBERON:0000998	94.90	gold quality
esophagus squamous epithelium	UBERON:0006920	94.61	gold quality
pericardium	UBERON:0002407	94.39	gold quality
gingival epithelium	UBERON:0001949	94.25	gold quality
bronchial epithelial cell	CL:0002328	94.12	gold quality
synovial joint	UBERON:0002217	94.12	gold quality
gingiva	UBERON:0001828	94.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

128 targeting CFAP97, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-141-3P	99.94	72.79	2421

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap97	ENSDARG00000056381
mus_musculus	Cfap97	ENSMUSG00000031631
rattus_norvegicus	Cfap97	ENSRNOG00000032192

Protein

Protein identifiers

Cilia- and flagella-associated protein 97 — Q9P2B7 (reviewed: Q9P2B7)

All UniProt accessions (3): A0A3B3IRJ5, Q9P2B7, D6RDU8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CFAP97 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9P2B7-1	1	yes
Q9P2B7-2	2

RefSeq proteins (2): NP_001278962, NP_065878* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029488	Hmw/CFAP97	Family
IPR038791	Cfap97/Hemingway	Family

Pfam: PF13879

UniProt features (29 total): compositionally biased region 10, modified residue 7, region of interest 5, splice variant 2, sequence variant 2, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2B7-F1	58.55	0.14

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 (7): 19, 133, 138, 139, 218, 248, 330

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): HORIUCHI_WTAP_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MARTINEZ_RB1_TARGETS_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, chr4q35, ZHANG_BREAST_CANCER_PROGENITORS_UP, MARTINEZ_RB1_AND_TP53_TARGETS_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, GCM_RAB10, NFE2L2.V2, CSHL1_TARGET_GENES, MAML1_TARGET_GENES, PCGF1_TARGET_GENES, SKIL_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1716 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP97	CFAP97D2	A0A1B0GU71	589
CFAP97	CFAP96	A7E2U8	518
CFAP97	TTLL1	O95922	457
CFAP97	FAM149A	A5PLN7	445
CFAP97	RBM18	Q96H35	440
CFAP97	RPH3AL	Q9UNE2	437
CFAP97	FAM32A	Q9Y421	427
CFAP97	UNC5D	Q6UXZ4	426
CFAP97	ADAM22	Q9P0K1	409
CFAP97	SORBS1	Q9BX66	396
CFAP97	STOX2	Q9P2F5	395
CFAP97	ELAVL4	P26378	391
CFAP97	PROSER3	Q2NL68	386
CFAP97	QRICH2	Q9H0J4	375
CFAP97	UBOX5	O94941	348
CFAP97	UFSP2	Q9NUQ7	348

IntAct

33 interactions, top by confidence:

A	B	Type	Score
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
Cdc23	BUB1B	psi-mi:“MI:0915”(physical association)	0.560
CDC27	CFAP97	psi-mi:“MI:0914”(association)	0.460
CFAP97	RRBP1	psi-mi:“MI:0915”(physical association)	0.400
PLA2G4F	CFAP97	psi-mi:“MI:0915”(physical association)	0.400
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
Cdc16	ANAPC15	psi-mi:“MI:0914”(association)	0.350
Cdc23	ANAPC15	psi-mi:“MI:0914”(association)	0.350
Cdc26		psi-mi:“MI:0914”(association)	0.350
Cdc26	PEX10	psi-mi:“MI:0914”(association)	0.350
Anapc2	ANAPC15	psi-mi:“MI:0914”(association)	0.350
ANAPC15		psi-mi:“MI:0914”(association)	0.350
CFAP97	CSNK2A1	psi-mi:“MI:0914”(association)	0.350
PCM1	SUPT5H	psi-mi:“MI:0914”(association)	0.350
CSNK2B	OSBPL8	psi-mi:“MI:0914”(association)	0.350
SFPQ	YLPM1	psi-mi:“MI:0914”(association)	0.350
TRMT1L	POLR3A	psi-mi:“MI:0914”(association)	0.350
APBA1	KIF2A	psi-mi:“MI:0914”(association)	0.350
KCNE3	PIK3R2	psi-mi:“MI:0914”(association)	0.350
ANAPC15	U2SURP	psi-mi:“MI:0914”(association)	0.350
FTL	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
KCNE3	TMEM131L	psi-mi:“MI:0914”(association)	0.350
CEP128	CCDC66	psi-mi:“MI:2364”(proximity)	0.270
LCA5	DVL2	psi-mi:“MI:2364”(proximity)	0.270
DCTN1	NACA	psi-mi:“MI:2364”(proximity)	0.270
LCA5	CCDC66	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (78): CFAP97 (Affinity Capture-Western), CFAP97 (Affinity Capture-MS), CFAP97 (Proximity Label-MS), CFAP97 (Proximity Label-MS), CFAP97 (Proximity Label-MS), CFAP97 (Proximity Label-MS), AP2A1 (Affinity Capture-MS), SLC25A4 (Affinity Capture-MS), CDC27 (Affinity Capture-MS), CDKN2A (Affinity Capture-MS), CLTA (Affinity Capture-MS), CSNK2A1 (Affinity Capture-MS), CSNK2A2 (Affinity Capture-MS), FLII (Affinity Capture-MS), HMGB2 (Affinity Capture-MS)

ESM2 similar proteins: A4IJ15, A5WUN7, A8T6P4, D4AEC2, E7F568, O42400, P28290, P57094, Q08AD1, Q08AZ1, Q09JY9, Q0VA20, Q27IV2, Q2KJH5, Q2MJV9, Q3KQW7, Q3MHH7, Q3TRR0, Q3UH68, Q3UHI0, Q4KM62, Q5DTV4, Q5NVK0, Q5RD75, Q5RHU7, Q5RJ80, Q5TID7, Q5U2Y9, Q5XG16, Q66H34, Q69ZW3, Q6GLU8, Q6IRN6, Q6ZPR1, Q7SXC6, Q7ZX27, Q801E2, Q8C1B1, Q8K1N2, Q8K298

Diamond homologs: A4IJ15, Q2KJH5, Q5RD75, Q66H34, Q6ZPR1, Q9P2B7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Cell Cycle Checkpoints	6	19.7×	1e-04
M Phase	5	12.2×	1e-03
Cell Cycle, Mitotic	5	8.9×	3e-03
Cell Cycle	6	8.0×	2e-03
Signaling by Rho GTPases	5	6.3×	8e-03
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	5	6.2×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
cell division	7	9.2×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	101
Likely benign	9
Benign	4

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
57066	GRCh38/hg38 4q35.1-35.2(chr4:183528264-188624331)x1	Pathogenic
625785	GRCh37/hg19 4q34.1-35.2(chr4:174610492-190427545)	Pathogenic

SpliceAI

1188 predictions. Top by Δscore:

Variant	Effect	Δscore
4:185162925:CCTGA:C	acceptor_loss	1.0000
4:185164023:GCTTA:G	donor_loss	1.0000
4:185164024:CTTAC:C	donor_loss	1.0000
4:185164027:A:AC	donor_gain	1.0000
4:185164027:AC:A	donor_loss	1.0000
4:185164028:C:CA	donor_gain	1.0000
4:185164028:CT:C	donor_gain	1.0000
4:185164028:CTT:C	donor_gain	1.0000
4:185164028:CTTA:C	donor_gain	1.0000
4:185164028:CTTAA:C	donor_gain	1.0000
4:185164031:A:AC	donor_gain	1.0000
4:185164032:A:C	donor_gain	1.0000
4:185164175:AAAGC:A	acceptor_gain	1.0000
4:185164179:CCT:C	acceptor_loss	1.0000
4:185164183:C:CT	acceptor_gain	1.0000
4:185164184:A:T	acceptor_gain	1.0000
4:185164185:A:AC	acceptor_gain	1.0000
4:185175782:TTA:T	donor_loss	1.0000
4:185175783:TA:T	donor_loss	1.0000
4:185175784:A:AC	donor_gain	1.0000
4:185175785:C:CC	donor_gain	1.0000
4:185175785:CCAA:C	donor_gain	1.0000
4:185175785:CCAAG:C	donor_gain	1.0000
4:185176047:AAAAG:A	acceptor_gain	1.0000
4:185176048:AAAG:A	acceptor_gain	1.0000
4:185176049:AAG:A	acceptor_gain	1.0000
4:185176050:AG:A	acceptor_gain	1.0000
4:185176052:C:CC	acceptor_gain	1.0000
4:185176065:C:CT	acceptor_gain	1.0000
4:185191208:TATAT:T	acceptor_gain	1.0000

AlphaMissense

3486 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:185164163:A:G	L446P	0.999
4:185175822:T:A	R428S	0.999
4:185175822:T:G	R428S	0.999
4:185175925:A:G	L394P	0.999
4:185164158:C:G	A448P	0.998
4:185164163:A:T	L446H	0.998
4:185175823:C:G	R428T	0.998
4:185175935:T:C	N391D	0.998
4:185175789:G:C	N439K	0.997
4:185175789:G:T	N439K	0.997
4:185175811:T:G	Q432P	0.997
4:185175969:G:C	F379L	0.997
4:185175969:G:T	F379L	0.997
4:185175971:A:G	F379L	0.997
4:185190148:A:G	L350S	0.997
4:185164118:A:G	L461P	0.996
4:185164131:G:T	R457S	0.996
4:185164165:C:A	R445S	0.996
4:185164165:C:G	R445S	0.996
4:185175791:T:C	N439D	0.996
4:185175802:A:C	I435S	0.996
4:185175824:T:C	R428G	0.996
4:185175913:A:G	L398P	0.996
4:185175934:T:C	N391S	0.996
4:185190151:A:G	L349P	0.996
4:185164103:C:G	R466P	0.995
4:185164172:A:G	L443S	0.995
4:185164179:C:G	A441P	0.995
4:185175970:A:G	F379S	0.995
4:185164154:A:T	V449E	0.994

dbSNP variants (sampled 300 via entrez): RS1000031449 (4:185161083 C>T), RS1000072148 (4:185167174 A>C), RS1000094375 (4:185193301 G>T), RS1000104312 (4:185182784 A>G), RS1000277135 (4:185187553 G>A), RS1000334341 (4:185175601 T>C), RS1000367207 (4:185175353 G>A), RS1000674607 (4:185177130 G>A,C), RS1000783296 (4:185183273 G>A), RS1000806024 (4:185209593 G>C), RS1000807457 (4:185162595 T>C,G), RS1000833907 (4:185170755 C>T), RS1000855650 (4:185180705 A>T), RS1000858384 (4:185162417 G>C), RS1000859997 (4:185209422 G>A,C)

Disease associations

OMIM: gene MIM:616047 | 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

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	8
Estradiol	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
trichostatin A	decreases expression	1
arsenite	decreases reaction, affects binding	1
sodium arsenite	decreases expression	1
perfluoro-n-nonanoic acid	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	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Caffeine	decreases phosphorylation	1
Doxorubicin	decreases expression	1
Ribonucleotides	affects binding	1
Tetrachlorodibenzodioxin	affects expression	1
Theophylline	increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	decreases methylation	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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