CFAP73

Summary

CFAP73 (cilia and flagella associated protein 73, HGNC:37100) is a protein-coding gene on chromosome 12q24.13, encoding Cilia- and flagella-associated protein 73 (A6NFT4). May play a role in ciliary/flagellar motility by regulating the assembly and the activity of axonemal inner dynein arm.

Predicted to enable dynein complex binding activity. Predicted to be involved in cilium movement and inner dynein arm assembly. Predicted to be located in axonemal doublet microtubule and motile cilium.

Source: NCBI Gene 387885 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 90 total — 2 pathogenic
• MANE Select transcript: NM_001144872

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37100
Approved symbol	CFAP73
Name	cilia and flagella associated protein 73
Location	12q24.13
Locus type	gene with protein product
Status	Approved
Aliases	MIA2
Ensembl gene	ENSG00000186710
Ensembl biotype	protein_coding
Entrez	387885

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 retained_intron

ENST00000335621, ENST00000550918, ENST00000551256, ENST00000865198, ENST00000865199, ENST00000865200, ENST00000865201, ENST00000865202, ENST00000949583

RefSeq mRNA: 1 — MANE Select: NM_001144872 NM_001144872

CCDS: CCDS44983

Canonical transcript exons

ENST00000335621 — 8 exons

Exon	Start	End
ENSE00001424124	113153208	113153408
ENSE00001426498	113152783	113152887
ENSE00001428878	113151918	113152023
ENSE00001561969	113149724	113149913
ENSE00002313940	113158701	113159276
ENSE00003496707	113155260	113155418
ENSE00003549083	113154414	113154635
ENSE00003586153	113157602	113157690

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 99.33.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0390 / max 15.2469, expressed in 7 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128145	0.0390	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.33	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.23	gold quality
nasal cavity epithelium	UBERON:0005384	90.21	silver quality
parotid gland	UBERON:0001831	87.94	silver quality
bronchial epithelial cell	CL:0002328	87.21	gold quality
bronchus	UBERON:0002185	86.57	gold quality
nasal cavity mucosa	UBERON:0001826	86.00	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	84.36	silver quality
fallopian tube	UBERON:0003889	81.39	gold quality
biceps brachii	UBERON:0001507	80.67	silver quality
cerebellar vermis	UBERON:0004720	80.60	gold quality
tendon of biceps brachii	UBERON:0008188	80.16	gold quality
caput epididymis	UBERON:0004358	79.77	gold quality
upper arm skin	UBERON:0004263	79.58	gold quality
heart right ventricle	UBERON:0002080	79.50	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	79.06	silver quality
kidney epithelium	UBERON:0004819	78.29	gold quality
right lung	UBERON:0002167	78.19	gold quality
trabecular bone tissue	UBERON:0002483	77.45	silver quality
tibialis anterior	UBERON:0001385	76.44	silver quality
vena cava	UBERON:0004087	76.42	silver quality
left uterine tube	UBERON:0001303	76.16	gold quality
oocyte	CL:0000023	76.06	gold quality
decidua	UBERON:0002450	76.04	silver quality
entorhinal cortex	UBERON:0002728	75.68	silver quality
cauda epididymis	UBERON:0004360	75.67	silver quality
cartilage tissue	UBERON:0002418	75.51	silver quality
postcentral gyrus	UBERON:0002581	75.48	silver quality
lateral nuclear group of thalamus	UBERON:0002736	75.47	gold quality
corpus epididymis	UBERON:0004359	75.36	silver quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	63.52
E-HCAD-4	yes	53.26
E-ANND-3	yes	11.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting CFAP73, 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-1184	99.99	68.19	1458
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-4688	99.48	64.68	828
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-3154	98.94	66.55	1455
HSA-MIR-7113-3P	98.75	65.71	1120
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-31-5P	98.58	68.35	1239
HSA-MIR-1291	96.28	65.89	1224
HSA-MIR-654-5P	96.07	66.18	1280
HSA-MIR-6775-3P	95.76	65.91	982
HSA-MIR-6850-5P	94.72	64.25	62

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap73	ENSDARG00000035550
mus_musculus	Cfap73	ENSMUSG00000094282
rattus_norvegicus	Cfap73	ENSRNOG00000056407

Paralogs (3): CCDC42 (ENSG00000161973), CFAP100 (ENSG00000163885), CCDC38 (ENSG00000165972)

Protein

Protein identifiers

Cilia- and flagella-associated protein 73 — A6NFT4 (reviewed: A6NFT4)

Alternative names: Coiled-coil domain-containing protein 42B

All UniProt accessions (2): A6NFT4, H0YHK5

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in ciliary/flagellar motility by regulating the assembly and the activity of axonemal inner dynein arm.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium axoneme.

Similarity. Belongs to the CFAP73 family.

RefSeq proteins (1): NP_001138344* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025252	DUF4200	Domain
IPR051147	CFAP_domain-containing	Family

Pfam: PF13863

UniProt features (3 total): coiled-coil region 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NFT4-F1	88.57	0.70

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 300 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, TAATAAT_MIR126, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, CHUANG_OXIDATIVE_STRESS_RESPONSE_UP, MORF_ATRX, GOBP_VESICLE_MEDIATED_TRANSPORT, HNF1_Q6, REACTOME_MEMBRANE_TRAFFICKING, GOBP_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM, GOBP_INNER_DYNEIN_ARM_ASSEMBLY, GOBP_AXONEMAL_DYNEIN_COMPLEX_ASSEMBLY, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, MYCMAX_01, DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN, GOBP_CILIUM_ORGANIZATION

GO Biological Process (2): cilium movement (GO:0003341), inner dynein arm assembly (GO:0036159)

GO Molecular Function (1): dynein complex binding (GO:0070840)

GO Cellular Component (6): motile cilium (GO:0031514), axonemal doublet microtubule (GO:0097545), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
microtubule-based movement	1
axonemal dynein complex assembly	1
protein-containing complex binding	1
cilium	1
axoneme	1
A axonemal microtubule	1
B axonemal microtubule	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

332 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP73	CCDC38	Q502W7	632
CFAP73	CFAP100	Q494V2	603
CFAP73	RITA1	Q96K30	533
CFAP73	RIMBP3B	A6NNM3	487
CFAP73	DRC10	Q96DY2	484
CFAP73	CCDC40	Q4G0X9	475
CFAP73	CCDC39	Q9UFE4	466
CFAP73	TDRD15	B5MCY1	463
CFAP73	CFAP157	Q5JU67	419
CFAP73	FAM174C	Q9BVV8	419
CFAP73	BRD10	Q5HYC2	418
CFAP73	PRSS37	A4D1T9	414
CFAP73	RIMBP3C	A6NJZ7	412
CFAP73	PPP1R42	Q7Z4L9	410
CFAP73	DRC5	Q5JU00	404

IntAct

2 interactions, top by confidence:

A	B	Type	Score
NFKB1	NFKB1	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): CCDC42B (Affinity Capture-MS), CCDC42B (Affinity Capture-RNA)

ESM2 similar proteins: A4FV37, A4IFI1, A5D8V7, A6NC98, A6NFT4, A6NGB0, A6QQM8, A9UQN0, B0BMJ2, B0BNK9, D3Z5T1, D6REC4, J3QPZ5, O00411, O60826, O94812, P0C7Q1, P0CW27, P86182, Q0P5D1, Q13515, Q15834, Q17Q97, Q1RMI8, Q2M329, Q3V3V9, Q494R4, Q4QRL3, Q571B6, Q58EX7, Q5BK61, Q5FVL4, Q5ND29, Q5SPX1, Q66H85, Q6F5E8, Q6NTM6, Q6PDY0, Q7TMK6, Q80ZJ8

Diamond homologs: A6NFT4, A6QQM8, A7S8T5, A9UQN0, B0BMJ2, J3QPZ5, Q5SV66, Q6NTM6, Q96M95, Q3KPZ2, M1V4Y8

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	2
Likely pathogenic	0
Uncertain significance	73
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1527733	GRCh37/hg19 12q24.13-24.21(chr12:113445811-114933860)	Pathogenic
155465	GRCh38/hg38 12q24.13-24.21(chr12:113077775-114372366)x1	Pathogenic

SpliceAI

1435 predictions. Top by Δscore:

Variant	Effect	Δscore
12:113149914:G:GG	donor_gain	1.0000
12:113151902:ACTT:A	acceptor_gain	1.0000
12:113152778:CCCA:C	acceptor_loss	1.0000
12:113152779:CCAG:C	acceptor_loss	1.0000
12:113152781:A:AG	acceptor_gain	1.0000
12:113152781:AGG:A	acceptor_loss	1.0000
12:113152782:G:GG	acceptor_gain	1.0000
12:113152782:GGT:G	acceptor_gain	1.0000
12:113152884:GCAG:G	donor_gain	1.0000
12:113152886:AG:A	donor_gain	1.0000
12:113152887:GG:G	donor_gain	1.0000
12:113152888:G:GG	donor_gain	1.0000
12:113153196:C:CA	acceptor_gain	1.0000
12:113153199:A:AG	acceptor_gain	1.0000
12:113154412:A:AG	acceptor_gain	1.0000
12:113154413:G:GG	acceptor_gain	1.0000
12:113154617:G:GT	donor_gain	1.0000
12:113154632:G:GG	donor_gain	1.0000
12:113155415:GCAC:G	donor_gain	1.0000
12:113155419:G:GG	donor_gain	1.0000
12:113149910:CTACG:C	donor_loss	0.9900
12:113149911:TACGT:T	donor_loss	0.9900
12:113149912:ACGT:A	donor_loss	0.9900
12:113149913:CGTG:C	donor_loss	0.9900
12:113149914:GTG:G	donor_loss	0.9900
12:113149915:T:G	donor_loss	0.9900
12:113149922:G:GT	donor_gain	0.9900
12:113149922:G:T	donor_gain	0.9900
12:113151895:A:AG	acceptor_gain	0.9900
12:113151896:C:G	acceptor_gain	0.9900

AlphaMissense

1955 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:113152870:T:C	F84L	0.931
12:113152872:T:A	F84L	0.931
12:113152872:T:G	F84L	0.931
12:113154444:T:C	F167L	0.918
12:113154446:C:A	F167L	0.918
12:113154446:C:G	F167L	0.918
12:113154414:T:C	F157L	0.909
12:113154416:C:A	F157L	0.909
12:113154416:C:G	F157L	0.909
12:113155344:T:C	F259L	0.908
12:113155346:C:A	F259L	0.908
12:113155346:C:G	F259L	0.908
12:113155279:T:C	I237T	0.906
12:113152879:T:C	F87L	0.888
12:113152881:T:A	F87L	0.888
12:113152881:T:G	F87L	0.888
12:113155290:G:C	A241P	0.882
12:113155269:T:A	W234R	0.868
12:113155269:T:C	W234R	0.868
12:113155293:G:C	A242P	0.844
12:113157611:T:C	F287L	0.838
12:113157613:C:A	F287L	0.838
12:113157613:C:G	F287L	0.838
12:113154612:G:C	A223P	0.823
12:113155271:G:C	W234C	0.814
12:113155271:G:T	W234C	0.814
12:113155263:T:C	S232P	0.811
12:113155279:T:G	I237S	0.806
12:113155329:G:C	A254P	0.803
12:113155314:G:A	G249R	0.802

dbSNP variants (sampled 300 via entrez): RS1000052514 (12:113151962 G>A), RS1000421181 (12:113158056 C>G), RS1000717434 (12:113151585 G>A,C), RS1000727679 (12:113149956 G>A,T), RS1001192300 (12:113150647 C>A), RS1001223434 (12:113150917 T>C), RS1001325356 (12:113150262 A>G), RS1001456707 (12:113153748 A>C), RS1001874273 (12:113157162 C>A), RS1001981048 (12:113150312 G>T), RS1002059435 (12:113156471 G>A,C), RS1002229291 (12:113149557 T>C), RS1003184934 (12:113148022 T>A,G), RS1003215943 (12:113147888 G>A), RS1003256585 (12:113155249 G>C)

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
GCST005951_2	Body mass index	9.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	1
perfluorooctanoic acid	decreases 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
Air Pollutants	increases abundance, increases expression	1
Formaldehyde	decreases expression	1
Phenylmercuric Acetate	affects cotreatment, decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases expression, increases methylation	1

Clinical trials (associated diseases)

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