FAM110A

Summary

FAM110A (family with sequence similarity 110 member A, HGNC:16188) is a protein-coding gene on chromosome 20p13, encoding Protein FAM110A (Q9BQ89).

Involved in mitotic spindle organization. Located in cytosol; microtubule cytoskeleton; and nucleus.

Source: NCBI Gene 83541 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_001042353

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16188
Approved symbol	FAM110A
Name	family with sequence similarity 110 member A
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	bA371L19.3
Ensembl gene	ENSG00000125898
Ensembl biotype	protein_coding
OMIM	611393
Entrez	83541

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 16 protein_coding

ENST00000246100, ENST00000304189, ENST00000381939, ENST00000381941, ENST00000505691, ENST00000541082, ENST00000902990, ENST00000902991, ENST00000902992, ENST00000922837, ENST00000922838, ENST00000922839, ENST00000922840, ENST00000922841, ENST00000922842, ENST00000956297

RefSeq mRNA: 6 — MANE Select: NM_001042353 NM_001042353, NM_001289145, NM_001289146, NM_001289147, NM_031424, NM_207121

CCDS: CCDS13008

Canonical transcript exons

ENST00000381941 — 2 exons

Exon	Start	End
ENSE00001490345	833715	833951
ENSE00003846359	844708	846277

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 94.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.9042 / max 447.4732, expressed in 1772 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
183067	5.3922	1283
183066	3.5716	1449
183071	2.9423	584
183073	1.8198	515
183070	1.4619	450
183068	1.3576	700
208964	0.2262	89
183072	0.0864	31
208963	0.0257	11
183069	0.0204	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	94.44	gold quality
granulocyte	CL:0000094	93.60	gold quality
skin of leg	UBERON:0001511	93.34	gold quality
lower esophagus mucosa	UBERON:0035834	93.13	gold quality
skin of abdomen	UBERON:0001416	92.27	gold quality
leukocyte	CL:0000738	91.78	gold quality
monocyte	CL:0000576	91.73	gold quality
zone of skin	UBERON:0000014	91.04	gold quality
esophagus mucosa	UBERON:0002469	89.04	gold quality
blood	UBERON:0000178	87.98	gold quality
oocyte	CL:0000023	86.26	gold quality
secondary oocyte	CL:0000655	85.27	gold quality
spleen	UBERON:0002106	84.91	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	84.86	gold quality
mucosa of transverse colon	UBERON:0004991	83.65	gold quality
minor salivary gland	UBERON:0001830	83.48	gold quality
cortical plate	UBERON:0005343	83.45	gold quality
mouth mucosa	UBERON:0003729	82.48	gold quality
nasal cavity mucosa	UBERON:0001826	81.31	gold quality
ganglionic eminence	UBERON:0004023	81.31	gold quality
saliva-secreting gland	UBERON:0001044	80.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.98	gold quality
vagina	UBERON:0000996	79.85	gold quality
right lung	UBERON:0002167	79.50	gold quality
upper lobe of left lung	UBERON:0008952	79.31	gold quality
ventricular zone	UBERON:0003053	79.20	gold quality
nipple	UBERON:0002030	78.59	gold quality
upper lobe of lung	UBERON:0008948	78.33	gold quality
esophagus	UBERON:0001043	78.21	gold quality
prostate gland	UBERON:0002367	78.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6911	yes	535.65
E-CURD-88	yes	11.74
E-ANND-3	yes	7.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting FAM110A, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-5589-5P	98.34	64.82	1148
HSA-MIR-6131	97.22	66.72	960
HSA-MIR-6836-3P	97.08	64.99	712
HSA-MIR-3152-5P	96.98	66.88	819
HSA-MIR-555	95.92	65.25	564

Literature-anchored findings (GeneRIF, showing 3)

• Protein with cell cycle-regulated expression and distinct conserved motifs, which localizes to centrosomes and spindle poles. (PMID:17499476)
• Pan-cancer analysis reveals potential of FAM110A as a prognostic and immunological biomarker in human cancer. (PMID:36923407)
• FAM110A promotes mitotic spindle formation by linking microtubules with actin cytoskeleton. (PMID:38995965)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam110a	ENSMUSG00000027459
rattus_norvegicus	Fam110a	ENSRNOG00000050946

Paralogs (3): FAM110B (ENSG00000169122), FAM110C (ENSG00000184731), FAM110D (ENSG00000197245)

Protein

Protein identifiers

Protein FAM110A — Q9BQ89 (reviewed: Q9BQ89)

All UniProt accessions (2): Q9BQ89, V9GZ26

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. May interact with CSPP1.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Spindle pole.

Tissue specificity. Detected in thyroid, lymph node, trachea, adrenal gland, bone marrow, spleen, thymus, prostate, and peripheral blood leukocyte. Detected at lower levels in stomach, testis and spinal cord.

Induction. Up-regulated in stimulated lymphocytes.

Similarity. Belongs to the FAM110 family.

RefSeq proteins (6): NP_001035812, NP_001276074, NP_001276075, NP_001276076, NP_113612, NP_997004 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025739	FAM110_N	Domain
IPR025740	FAM110	Family
IPR025741	FAM110_C	Domain

Pfam: PF14160, PF14161

UniProt features (8 total): compositionally biased region 4, region of interest 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQ89-F1	62.24	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GCAAGGA_MIR502, FOXO1_01, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, GOCC_MICROTUBULE_ORGANIZING_CENTER, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6, FISCHER_G2_M_CELL_CYCLE, TGCTGAY_UNKNOWN, GOCC_CENTROSOME, LIAO_METASTASIS, GOBP_MITOTIC_CELL_CYCLE, PU1_Q6, RYTTCCTG_ETS2_B

GO Biological Process (1): mitotic spindle organization (GO:0007052)

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

GO Cellular Component (8): spindle pole (GO:0000922), nucleus (GO:0005634), centrosome (GO:0005813), cytosol (GO:0005829), spindle microtubule (GO:0005876), cell cortex (GO:0005938), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
spindle	2
cytoplasm	2
mitotic cell cycle	1
spindle organization	1
microtubule cytoskeleton organization involved in mitosis	1
binding	1
intracellular membrane-bounded organelle	1
centriole	1
microtubule organizing center	1
microtubule	1
cell periphery	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

472 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM110A	CSPP1	Q1MSJ5	947
FAM110A	TM2D2	Q9BX73	511
FAM110A	ZMAT4	Q9H898	489
FAM110A	ZDHHC18	Q9NUE0	475
FAM110A	PLEKHA2	Q9HB19	470
FAM110A	KCTD3	Q9Y597	463
FAM110A	GPANK1	O95872	451
FAM110A	SMIM13	P0DJ93	447
FAM110A	TAFA1	Q7Z5A9	437
FAM110A	SNX29	Q8TEQ0	414
FAM110A	RPAP3	Q9H6T3	408
FAM110A	LMAN1	P49257	407
FAM110A	TACC1	O75410	395
FAM110A	TYW1B	Q6NUM6	395
FAM110A	ANKRD9	Q96BM1	391

IntAct

242 interactions, top by confidence:

A	B	Type	Score
KRT15	FAM110A	psi-mi:“MI:0915”(physical association)	0.720
FAM110A	TRIM23	psi-mi:“MI:0915”(physical association)	0.720
GOLGA2	FAM110A	psi-mi:“MI:0915”(physical association)	0.720
MKRN3	FAM110A	psi-mi:“MI:0915”(physical association)	0.720
KRT31	FAM110A	psi-mi:“MI:0915”(physical association)	0.720
FAM110A	RINT1	psi-mi:“MI:0915”(physical association)	0.720
FAM110A	USHBP1	psi-mi:“MI:0915”(physical association)	0.720
TRIM54	FAM110A	psi-mi:“MI:0915”(physical association)	0.720
FAM110A	KRT15	psi-mi:“MI:0915”(physical association)	0.720
FAM110A	GOLGA2	psi-mi:“MI:0915”(physical association)	0.720
FAM110A	KRT31	psi-mi:“MI:0915”(physical association)	0.720
USHBP1	FAM110A	psi-mi:“MI:0915”(physical association)	0.720
FAM110A	TRIM54	psi-mi:“MI:0915”(physical association)	0.720
FAM110A	MKRN3	psi-mi:“MI:0915”(physical association)	0.720
TRIM23	FAM110A	psi-mi:“MI:0915”(physical association)	0.720
RINT1	FAM110A	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (114): FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), FAM110A (Two-hybrid), USHBP1 (Two-hybrid), TRIM69 (Two-hybrid), FAM110A (Two-hybrid)

ESM2 similar proteins: A2A9T0, A2AEV7, A2AHG0, A5PKL7, A6H7I7, A6NCL7, A6NKL6, B8ZZ34, D3ZZN9, J3QNX5, O60299, Q0PHV7, Q1W6H9, Q2KJ38, Q2M3G4, Q2M3V2, Q3LUD4, Q3SX20, Q4KLY2, Q4KMQ1, Q4QRD7, Q53LP3, Q58DG5, Q5RKJ0, Q5SW24, Q6DG50, Q6NUJ5, Q6NY19, Q6PJ61, Q6ZW31, Q7TN08, Q7TNF9, Q80X91, Q8BLS7, Q8CHM3, Q8IX07, Q8IXH6, Q8K1Q4, Q8R184, Q8TAY7

Diamond homologs: A6H7I7, Q1W6H9, Q58DG5, Q80X91, Q8R184, Q8TAY7, Q8VE94, Q9BQ89, Q2KJ38, Q4QRD7, Q5BJX5, Q5R5R3, Q5RKJ0, Q8C739, Q8TC76

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 98 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
Formation of the cornified envelope	7	10.4×	1e-03
Keratinization	8	7.5×	1e-03
CDC42 GTPase cycle	6	7.3×	7e-03
RHO GTPase cycle	7	7.1×	3e-03
Signaling by Rho GTPases	9	5.2×	3e-03
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	9	5.1×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
morphogenesis of an epithelium	7	27.4×	4e-06
ephrin receptor signaling pathway	5	19.5×	7e-04
intermediate filament organization	7	19.1×	2e-05
epithelial cell differentiation	7	14.0×	1e-04
protein transport	11	5.5×	7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

430 predictions. Top by Δscore:

Variant	Effect	Δscore
20:833949:CAGGT:C	donor_loss	0.9900
20:833950:AG:A	donor_loss	0.9900
20:833951:GGTGA:G	donor_loss	0.9900
20:833952:G:A	donor_loss	0.9900
20:833953:T:G	donor_loss	0.9900
20:844707:GCA:G	acceptor_gain	0.9900
20:844707:GCAGT:G	acceptor_gain	0.9900
20:844706:A:AG	acceptor_gain	0.9800
20:844707:G:GG	acceptor_gain	0.9800
20:844707:GC:G	acceptor_gain	0.9800
20:844703:TGCAG:T	acceptor_loss	0.9600
20:844707:G:A	acceptor_loss	0.9600
20:841312:GCCGG:G	donor_gain	0.9500
20:844703:T:TA	acceptor_gain	0.9400
20:842106:G:GT	donor_gain	0.9300
20:842638:G:GA	donor_gain	0.9300
20:844710:G:GA	acceptor_gain	0.9300
20:833827:TGCCC:T	donor_gain	0.9100
20:842107:A:T	donor_gain	0.9100
20:834205:T:TA	donor_gain	0.8900
20:834206:A:AA	donor_gain	0.8900
20:834123:TTC:T	donor_gain	0.8600
20:839452:G:GC	acceptor_gain	0.8600
20:842670:A:G	donor_gain	0.8400
20:844709:A:AG	acceptor_gain	0.8400
20:841565:G:GT	donor_gain	0.8300
20:841586:GGATC:G	donor_gain	0.8100
20:833952:G:GG	donor_gain	0.8000
20:833967:G:A	donor_gain	0.8000
20:841316:GGTA:G	donor_loss	0.8000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000115395 (20:842664 G>A), RS1000560747 (20:832291 T>C,G), RS1001409298 (20:837439 C>T), RS1001497506 (20:844530 G>A,C,T), RS1001503030 (20:833619 C>T), RS1001651615 (20:839806 C>A,G,T), RS1001887631 (20:834442 C>G,T), RS1001931434 (20:841401 G>A), RS1002002112 (20:839111 TG>T,TGG), RS1002184439 (20:833761 C>T), RS1002459505 (20:839431 A>G), RS1002950162 (20:833847 C>T), RS1003056925 (20:840958 G>T), RS1003150359 (20:846735 G>A,C), RS1003661329 (20:842416 C>G)

Disease associations

OMIM: gene MIM:611393 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001762_538	Obesity-related traits	7.000000e-06
GCST008860_36	Prostate cancer	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005191	waist height ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	affects cotreatment, decreases reaction, increases expression, decreases expression, increases abundance	3
sodium arsenite	decreases expression, increases abundance, increases expression	2
Benzo(a)pyrene	increases expression, increases methylation, affects methylation	2
Valproic Acid	affects expression, increases methylation	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
propionaldehyde	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
manganese chloride	increases abundance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
abrine	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Vehicle Emissions	decreases reaction, increases expression	1
Calcitriol	increases expression	1
Carbamazepine	affects expression	1
Gallic Acid	increases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Manganese	increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Naled	affects expression	1
Phthalic Acids	increases methylation	1
Polycyclic Aromatic Hydrocarbons	increases abundance, increases expression, affects cotreatment	1
Smoke	decreases expression	1

Clinical trials (associated diseases)

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