CFAP144

Summary

CFAP144 (cilia and flagella associated protein 144, HGNC:34347) is a protein-coding gene on chromosome 1p34.2, encoding Cilia- and flagella-associated protein 144 (A6NL82). Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating.

Enables microtubule binding activity. Predicted to be involved in flagellated sperm motility. Located in axonemal microtubule.

Source: NCBI Gene 440585 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_001101376

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34347
Approved symbol	CFAP144
Name	cilia and flagella associated protein 144
Location	1p34.2
Locus type	gene with protein product
Status	Approved
Aliases	LOC440585, hCG23177
Ensembl gene	ENSG00000186973
Ensembl biotype	protein_coding
OMIM	621114
Entrez	440585

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000335282, ENST00000409337, ENST00000409396, ENST00000410025, ENST00000410048, ENST00000481753, ENST00000940879

RefSeq mRNA: 1 — MANE Select: NM_001101376 NM_001101376

CCDS: CCDS44126

Canonical transcript exons

ENST00000335282 — 4 exons

Exon	Start	End
ENSE00001582379	43147904	43148084
ENSE00003472264	43156206	43156396
ENSE00003533174	43150761	43150820
ENSE00003533471	43152828	43152931

Expression profiles

Bgee: expression breadth ubiquitous, 123 present calls, max score 99.50.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3957 / max 66.4999, expressed in 96 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2493	0.3718	93
2494	0.0238	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.50	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.41	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.47	gold quality
fallopian tube	UBERON:0003889	90.43	gold quality
pituitary gland	UBERON:0000007	87.27	gold quality
adenohypophysis	UBERON:0002196	85.95	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.77	gold quality
right lung	UBERON:0002167	83.69	gold quality
right testis	UBERON:0004534	81.35	gold quality
left testis	UBERON:0004533	80.96	gold quality
testis	UBERON:0000473	80.52	gold quality
skin of abdomen	UBERON:0001416	78.95	gold quality
left uterine tube	UBERON:0001303	78.45	gold quality
prostate gland	UBERON:0002367	77.99	gold quality
zone of skin	UBERON:0000014	77.80	gold quality
skin of leg	UBERON:0001511	77.06	gold quality
hypothalamus	UBERON:0001898	75.43	gold quality
lower esophagus mucosa	UBERON:0035834	74.77	gold quality
esophagus mucosa	UBERON:0002469	74.27	gold quality
Ammon’s horn	UBERON:0001954	72.08	gold quality
endocervix	UBERON:0000458	70.21	gold quality
vagina	UBERON:0000996	70.07	gold quality
lung	UBERON:0002048	69.86	gold quality
metanephros cortex	UBERON:0010533	68.90	gold quality
caudate nucleus	UBERON:0001873	68.82	gold quality
cortex of kidney	UBERON:0001225	68.06	gold quality
endometrium	UBERON:0001295	67.86	gold quality
nucleus accumbens	UBERON:0001882	67.86	gold quality
adult mammalian kidney	UBERON:0000082	66.21	gold quality
upper lobe of left lung	UBERON:0008952	66.16	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 12.

Experiment	Marker?	Max mean expression
E-HCAD-15	yes	2689.30
E-HCAD-1	yes	2238.71
E-MTAB-8221	yes	2167.84
E-MTAB-10283	yes	1660.67
E-MTAB-6701	yes	1486.18
E-CURD-114	yes	1296.49
E-MTAB-10287	yes	1228.33
E-HCAD-38	yes	1025.85
E-MTAB-9154	yes	926.61
E-GEOD-130148	yes	16.48
E-MTAB-9388	yes	7.84
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Whole exome sequencing revealed a nonsense variant (c.377G>A; p.W126*) in FAM183A, a novel candidate gene for autosomal recessive intellectual disability. (PMID:30500859)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap144	ENSDARG00000087144
mus_musculus	Cfap144	ENSMUSG00000049154
rattus_norvegicus	Cfap144	ENSRNOG00000002873

Paralogs (1): CFAP144P1 (ENSG00000164556)

Protein

Protein identifiers

Cilia- and flagella-associated protein 144 — A6NL82 (reviewed: A6NL82)

Alternative names: Protein FAM183A

All UniProt accessions (4): A6NL82, B7ZBL6, B7ZBL7, B7ZBL9

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.

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

Similarity. Belongs to the CFAP144 family.

RefSeq proteins (1): NP_001094846* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029214	CFAP144	Family

Pfam: PF14886

UniProt features (2 total): chain 1, region of interest 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-A6NL82-F1	79.41	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 53 (showing top): DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, GOBP_CILIUM_MOVEMENT, chr1p34, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP, GOCC_CYTOPLASMIC_REGION, GOCC_MOTILE_CILIUM, GOCC_CILIARY_BASE, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, GOMF_CYTOSKELETAL_PROTEIN_BINDING, MADAN_DPPA4_TARGETS

GO Biological Process (1): flagellated sperm motility (GO:0030317)

GO Molecular Function (1): microtubule binding (GO:0008017)

GO Cellular Component (9): axonemal microtubule (GO:0005879), sperm flagellum (GO:0036126), ciliary base (GO:0097546), axonemal B tubule inner sheath (GO:0160112), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), 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	2
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
tubulin binding	1
cytoplasmic microtubule	1
axoneme	1
9+2 motile cilium	1
ciliary transition zone	1
ciliary transition fiber	1
A axonemal microtubule	1
axonemal microtubule doublet inner sheath	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

282 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP144	TXNRD3	Q86VQ6	714
CFAP144	RLF	Q13129	566
CFAP144	VWA3A	A6NCI4	540
CFAP144	DRC10	Q96DY2	540
CFAP144	ZNF624	Q9P2J8	514
CFAP144	C1orf50	Q9BV19	506
CFAP144	MYCBPAP	Q8TBZ2	498
CFAP144	EFCAB6	Q5THR3	471
CFAP144	DRC5	Q5JU00	452
CFAP144	TMEM269	A0A1B0GVZ9	447
CFAP144	RIBC2	Q9H4K1	443
CFAP144	ARMC3	Q5W041	433
CFAP144	CCDC30	Q5VVM6	419
CFAP144	TEKT4	Q8WW24	403
CFAP144	PRSS22	Q9GZN4	399
CFAP144	ZNF691	Q5VV52	399

IntAct

0 interactions, top by confidence:

BioGRID (1): LAMTOR1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A087WRI3, A2BFC9, A2RRW4, A4QMS7, A6NJV1, A6NL82, A6QPC0, A6QQ68, A8E4X8, A8E5W8, A8QW39, A9JS51, D6REC4, F1P3Y5, G3X6E2, P0C875, Q0VB26, Q1MSJ5, Q2IA00, Q2T9Q3, Q2TA11, Q3UY96, Q494V2, Q497Q6, Q4KKZ1, Q4QR77, Q4R5Y0, Q4R8V8, Q5NC57, Q5ZIH9, Q6J272, Q6PII3, Q6ZQR2, Q6ZVS7, Q7Z4T9, Q8CFW7, Q8N1D5, Q8N6G2, Q8WW14, Q95LR0

Diamond homologs: A6NL82, A8QW39, F1P3Y5, Q5NC57, Q6ZVS7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	13
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

603 predictions. Top by Δscore:

Variant	Effect	Δscore
1:43148030:GAGC:G	donor_gain	1.0000
1:43148033:C:G	donor_gain	1.0000
1:43148059:G:GG	donor_gain	1.0000
1:43148083:GA:G	donor_gain	1.0000
1:43148085:G:GG	donor_gain	1.0000
1:43148056:G:GT	donor_gain	0.9900
1:43150759:A:AG	acceptor_gain	0.9900
1:43150760:G:GG	acceptor_gain	0.9900
1:43150760:GTTC:G	acceptor_gain	0.9900
1:43148056:GCA:G	donor_gain	0.9800
1:43148066:G:GG	donor_gain	0.9800
1:43148082:AGA:A	donor_gain	0.9800
1:43148083:GAG:G	donor_gain	0.9800
1:43150817:GATG:G	donor_gain	0.9800
1:43148080:C:T	donor_gain	0.9700
1:43150821:G:GG	donor_gain	0.9700
1:43155390:G:GT	donor_gain	0.9700
1:43148065:C:G	donor_gain	0.9600
1:43148070:A:G	donor_gain	0.9600
1:43150819:TGGTA:T	donor_loss	0.9600
1:43150820:GGT:G	donor_loss	0.9600
1:43150821:G:T	donor_loss	0.9600
1:43150822:T:TC	donor_loss	0.9600
1:43150823:AA:A	donor_loss	0.9600
1:43148069:A:AG	donor_gain	0.9400
1:43150755:TTCTA:T	acceptor_gain	0.9400
1:43150756:TCTAG:T	acceptor_gain	0.9400
1:43150757:CTAG:C	acceptor_gain	0.9400
1:43150758:TA:T	acceptor_gain	0.9400
1:43152905:G:GT	donor_gain	0.9300

AlphaMissense

888 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:43152914:T:A	W94R	0.920
1:43152914:T:C	W94R	0.920
1:43152833:T:C	F67L	0.909
1:43152835:T:A	F67L	0.909
1:43152835:T:G	F67L	0.909
1:43150780:G:C	K51N	0.908
1:43150780:G:T	K51N	0.908
1:43148071:T:A	N40K	0.895
1:43148071:T:G	N40K	0.895
1:43152916:G:C	W94C	0.889
1:43152916:G:T	W94C	0.889
1:43150779:A:C	K51T	0.871
1:43150778:A:G	K51E	0.858
1:43156242:T:C	F112L	0.834
1:43156244:C:A	F112L	0.834
1:43156244:C:G	F112L	0.834
1:43148029:G:C	K26N	0.832
1:43148029:G:T	K26N	0.832
1:43148034:T:C	L28P	0.829
1:43156232:G:C	R108S	0.820
1:43156232:G:T	R108S	0.820
1:43148007:T:C	I19T	0.817
1:43152834:T:C	F67S	0.815
1:43152915:G:T	W94L	0.807
1:43148037:G:C	R29P	0.792
1:43148060:T:G	Y37D	0.788
1:43148013:G:C	R21P	0.785
1:43152915:G:C	W94S	0.785
1:43148061:A:C	Y37S	0.781
1:43148043:A:C	Q31P	0.779

dbSNP variants (sampled 300 via entrez): RS1000486698 (1:43151714 T>G), RS1000669947 (1:43146750 T>C), RS1000763138 (1:43146658 A>T), RS1000928324 (1:43147097 A>G), RS1001192168 (1:43152224 A>G), RS1001669582 (1:43146277 T>C), RS1001713471 (1:43145701 T>C), RS1001853298 (1:43153695 A>G), RS1001903346 (1:43152257 A>G), RS1002196667 (1:43154192 A>G), RS1002539001 (1:43142821 G>T), RS1003056306 (1:43142670 G>T), RS1003108520 (1:43142314 G>A,C), RS1003194992 (1:43155705 C>A,G), RS1003263125 (1:43148590 A>G)

Disease associations

OMIM: gene MIM:621114 | 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

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

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Cisplatin	affects cotreatment, increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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