FLACC1

Summary

FLACC1 (flagellum associated containing coiled-coil domains 1, HGNC:14439) is a protein-coding gene on chromosome 2q33.1, encoding Flagellum-associated coiled-coil domain-containing protein 1 (Q96Q35).

Predicted to be located in cytoplasmic vesicle and outer dense fiber. Predicted to be active in cytoplasm.

Source: NCBI Gene 130540 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 80 total
• MANE Select transcript: NM_001127391

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14439
Approved symbol	FLACC1
Name	flagellum associated containing coiled-coil domains 1
Location	2q33.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000155749
Ensembl biotype	protein_coding
OMIM	619796
Entrez	130540

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000286190, ENST00000392257, ENST00000405148, ENST00000415745, ENST00000418364, ENST00000425488, ENST00000439709, ENST00000448967, ENST00000494171, ENST00000494223

RefSeq mRNA: 3 — MANE Select: NM_001127391 NM_001127391, NM_001289993, NM_139163

CCDS: CCDS2346, CCDS46488

Canonical transcript exons

ENST00000392257 — 15 exons

Exon	Start	End
ENSE00001076302	201288271	201288781
ENSE00001511250	201289696	201289785
ENSE00003476532	201289457	201289566
ENSE00003497193	201348254	201348302
ENSE00003508276	201342370	201342431
ENSE00003535634	201346542	201346675
ENSE00003545149	201309151	201309250
ENSE00003546406	201351292	201351451
ENSE00003569041	201344170	201344263
ENSE00003570069	201330736	201330833
ENSE00003623865	201350711	201350782
ENSE00003624320	201307519	201307622
ENSE00003670033	201299238	201299300
ENSE00003679717	201330470	201330522
ENSE00003904935	201356982	201357345

Expression profiles

Bgee: expression breadth ubiquitous, 168 present calls, max score 96.25.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1696 / max 32.2510, expressed in 51 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
33219	0.1426	49
33220	0.0271	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	96.25	gold quality
bronchial epithelial cell	CL:0002328	88.57	gold quality
bronchus	UBERON:0002185	86.42	gold quality
mucosa of paranasal sinus	UBERON:0005030	84.84	gold quality
left testis	UBERON:0004533	83.91	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.90	gold quality
right testis	UBERON:0004534	83.02	gold quality
testis	UBERON:0000473	81.41	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	79.92	gold quality
descending thoracic aorta	UBERON:0002345	77.71	gold quality
cardiac muscle of right atrium	UBERON:0003379	77.17	gold quality
heart left ventricle	UBERON:0002084	77.08	gold quality
left ventricle myocardium	UBERON:0006566	77.05	gold quality
ascending aorta	UBERON:0001496	76.65	gold quality
thoracic aorta	UBERON:0001515	76.52	gold quality
cardiac ventricle	UBERON:0002082	76.38	gold quality
calcaneal tendon	UBERON:0003701	76.00	gold quality
apex of heart	UBERON:0002098	75.72	gold quality
right atrium auricular region	UBERON:0006631	75.48	gold quality
cardiac atrium	UBERON:0002081	74.97	gold quality
right lung	UBERON:0002167	74.75	gold quality
bone marrow cell	CL:0002092	74.71	gold quality
sural nerve	UBERON:0015488	74.70	gold quality
heart	UBERON:0000948	74.53	gold quality
aorta	UBERON:0000947	74.21	gold quality
fallopian tube	UBERON:0003889	73.35	gold quality
left coronary artery	UBERON:0001626	72.95	gold quality
lower esophagus muscularis layer	UBERON:0035833	72.86	gold quality
lower esophagus	UBERON:0013473	72.79	gold quality
popliteal artery	UBERON:0002250	72.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting FLACC1, 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-150-5P	99.99	66.69	1976
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6501-3P	98.71	67.45	1480
HSA-MIR-676-5P	98.49	68.87	1492
HSA-MIR-6831-5P	98.26	67.20	990
HSA-MIR-3927-3P	97.68	66.76	892
HSA-MIR-5189-3P	97.52	66.33	487
HSA-MIR-6736-3P	96.98	65.22	1342

Literature-anchored findings (GeneRIF, showing 2)

• Genome-wide association studies show a significant association between the intronic SNP rs1830298 in ALS2CR12 gene and breast cancer; further expression studies suggest that CASP8 might be the target gene. (PMID:25168388)
• rs13014235 is associated with susceptibility to cutaneous basal cell carcinoma. (PMID:25855136)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
mus_musculus	Flacc1	ENSMUSG00000047528
rattus_norvegicus	Flacc1	ENSRNOG00000024917
caenorhabditis_elegans		WBGENE00007131
caenorhabditis_elegans		WBGENE00007132
caenorhabditis_elegans		WBGENE00007134
caenorhabditis_elegans	pals-3	WBGENE00007657
caenorhabditis_elegans	pals-5	WBGENE00007659
caenorhabditis_elegans	pals-6	WBGENE00007660
caenorhabditis_elegans	pals-13	WBGENE00012505

Protein

Protein identifiers

Flagellum-associated coiled-coil domain-containing protein 1 — Q96Q35 (reviewed: Q96Q35)

Alternative names: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 12 protein

All UniProt accessions (4): Q96Q35, C9JTY0, C9JZS0, H7C1T5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Cytoplasmic granule. Cell projection. Cilium. Flagellum.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96Q35-1	1	yes
Q96Q35-2	2

RefSeq proteins (3): NP_001120863, NP_001276922, NP_631902 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026674	FLACC1	Family

UniProt features (9 total): coiled-coil region 3, chain 1, region of interest 1, compositionally biased region 1, modified residue 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96Q35-F1	75.95	0.47

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): 376

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): GOCC_MOTILE_CILIUM, GOCC_CILIUM, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, GOCC_OUTER_DENSE_FIBER, GOCC_9PLUS2_MOTILE_CILIUM, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER, SRSF9_TARGET_GENES, MIR1250_3P, MIR4276, GSE14308_TH2_VS_TH1_DN, BLANCO_MELO_MERS_COV_INFECTION_MCR5_CELLS_UP, GSE15767_MED_VS_SCS_MAC_LN_UP, DESCARTES_FETAL_INTESTINE_ERYTHROBLASTS

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (7): outer dense fiber (GO:0001520), cytoplasm (GO:0005737), cytoplasmic vesicle (GO:0031410), sperm flagellum (GO:0036126), 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	2
binding	1
sperm flagellum	1
polymeric cytoskeletal fiber	1
intracellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1
9+2 motile cilium	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

336 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FLACC1	CATSPERT	Q53TS8	511
FLACC1	ZNF404	Q494X3	480
FLACC1	ATP6AP1L	Q52LC2	476
FLACC1	TRAK2	O60296	448
FLACC1	LRRC37A2	A6NM11	445
FLACC1	LRRC37A	A6NMS7	444
FLACC1	LRRC37A3	O60309	434
FLACC1	ZNF155	Q12901	431
FLACC1	CASP8	Q14790	419
FLACC1	PLEKHD1	A6NEE1	404
FLACC1	RCCD1	A6NED2	396
FLACC1	BABAM1	Q9NWV8	391
FLACC1	ANKRD34A	Q69YU3	372
FLACC1	ABHD8	Q96I13	371
FLACC1	PPIL3	Q9H2H8	371

IntAct

24 interactions, top by confidence:

A	B	Type	Score
SULT2B1	FLACC1	psi-mi:“MI:0915”(physical association)	0.760
FLACC1	SULT2B1	psi-mi:“MI:0915”(physical association)	0.760
FLACC1	STK16	psi-mi:“MI:0915”(physical association)	0.560
TCL1A	FLACC1	psi-mi:“MI:0915”(physical association)	0.560
TXNDC5	FLACC1	psi-mi:“MI:0915”(physical association)	0.560
FLACC1	TCL1A	psi-mi:“MI:0915”(physical association)	0.560
FLACC1	TXNDC5	psi-mi:“MI:0915”(physical association)	0.560
FLACC1	SRC	psi-mi:“MI:0915”(physical association)	0.400
FLACC1	PIK3R1	psi-mi:“MI:0915”(physical association)	0.400
FLACC1	SPTAN1	psi-mi:“MI:0915”(physical association)	0.400
FLACC1	CLTA	psi-mi:“MI:0915”(physical association)	0.400
FLACC1	MTUS2	psi-mi:“MI:0915”(physical association)	0.370
FLACC1	SNX3	psi-mi:“MI:0914”(association)	0.350

BioGRID (42): ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), SULT2B1 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid), ALS2CR12 (Two-hybrid)

ESM2 similar proteins: A1L3H4, A5A777, A6H754, A7YY97, A9ULR1, B2GV52, C7GUN6, D3ZNV2, P05531, P0CAP1, P33716, P57679, P70281, Q03954, Q0IHJ3, Q28HY7, Q32L59, Q3UIJ9, Q4R764, Q4V9P3, Q58CS6, Q5EB94, Q5I0J4, Q5RA87, Q5XIC3, Q5ZK77, Q60547, Q60595, Q61806, Q63520, Q640Z7, Q6AY08, Q6CQ94, Q6NPG7, Q6P205, Q7L3B6, Q80Y56, Q810N9, Q8BXX9, Q8GYM3

Diamond homologs: Q6AY08, Q8BVM7, Q96Q35

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2198 predictions. Top by Δscore:

Variant	Effect	Δscore
2:201288782:C:CC	acceptor_gain	1.0000
2:201289428:A:AC	donor_gain	1.0000
2:201289429:G:C	donor_gain	1.0000
2:201289455:A:AC	donor_gain	1.0000
2:201289456:C:CC	donor_gain	1.0000
2:201289458:T:TA	donor_gain	1.0000
2:201289475:T:TA	donor_gain	1.0000
2:201289691:CTCA:C	donor_loss	1.0000
2:201289692:TCAC:T	donor_loss	1.0000
2:201289693:CA:C	donor_loss	1.0000
2:201289695:CCT:C	donor_gain	1.0000
2:201307514:GTTA:G	donor_loss	1.0000
2:201307515:TTAC:T	donor_loss	1.0000
2:201307516:TAC:T	donor_loss	1.0000
2:201307517:AC:A	donor_loss	1.0000
2:201307518:C:A	donor_loss	1.0000
2:201307520:T:TA	donor_gain	1.0000
2:201307623:C:CC	acceptor_gain	1.0000
2:201309143:GTACT:G	donor_loss	1.0000
2:201309147:TCACT:T	donor_loss	1.0000
2:201309148:CACTT:C	donor_loss	1.0000
2:201309149:A:AC	donor_gain	1.0000
2:201309149:ACTTT:A	donor_loss	1.0000
2:201309150:C:CA	donor_gain	1.0000
2:201309150:CT:C	donor_gain	1.0000
2:201309150:CTTT:C	donor_gain	1.0000
2:201309150:CTTTG:C	donor_gain	1.0000
2:201309246:CTGTC:C	acceptor_gain	1.0000
2:201330739:G:C	donor_gain	1.0000
2:201344163:CACT:C	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000037238 (2:201324842 G>A), RS1000096649 (2:201302455 A>G), RS1000104899 (2:201332172 T>C), RS1000200445 (2:201312296 T>A), RS1000211649 (2:201359608 T>C), RS1000228137 (2:201304914 T>C), RS1000280238 (2:201305092 A>T), RS1000295416 (2:201352621 T>G), RS1000376154 (2:201339277 T>C), RS1000391532 (2:201291134 C>T), RS1000470905 (2:201330182 G>A), RS1000523009 (2:201330459 G>A,C,T), RS1000551051 (2:201348500 C>T), RS1000558840 (2:201302582 T>C), RS1000694243 (2:201291886 C>G,T)

Disease associations

OMIM: gene MIM:619796 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST002568_7	Esophageal squamous cell carcinoma	4.000000e-13
GCST002842_11	Basal cell carcinoma	2.000000e-09
GCST003726_11	Basal cell carcinoma	7.000000e-19
GCST004607_249	Plateletcrit	1.000000e-09
GCST004632_137	Lymphocyte percentage of white cells	1.000000e-12
GCST004633_110	Neutrophil percentage of white cells	7.000000e-12
GCST004988_16	Breast cancer	2.000000e-16
GCST005896_50	Non-melanoma skin cancer	2.000000e-13
GCST008870_5	Keratinocyte cancer (MTAG)	2.000000e-48
GCST008871_65	Basal cell carcinoma	5.000000e-55
GCST008872_6	Squamous cell carcinoma	2.000000e-07
GCST010148_4	Cutaneous squamous cell carcinoma	3.000000e-09
GCST010244_357	Triglyceride levels	4.000000e-08
GCST011011_53	Youthful appearance (self-reported)	2.000000e-09
GCST90002388_307	Lymphocyte count	1.000000e-40
GCST90002389_135	Lymphocyte percentage of white cells	1.000000e-19
GCST90002402_285	Platelet count	1.000000e-18

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0007985	platelet crit
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0007990	neutrophil percentage of leukocytes
EFO:0009260	non-melanoma skin carcinoma
EFO:0010176	keratinocyte carcinoma
EFO:1001927	cutaneous squamous cell carcinoma
EFO:0004530	triglyceride measurement
EFO:0004587	lymphocyte count
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Smoke	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
sotorasib	decreases expression, affects cotreatment	1
triphenyl phosphate	affects expression	1
trichostatin A	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
trametinib	affects cotreatment, decreases expression	1
(+)-JQ1 compound	increases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression	1
Cisplatin	increases expression	1
Doxorubicin	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1QC	HAP1 ALS2CR12 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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