FAM110C

Summary

FAM110C (family with sequence similarity 110 member C, HGNC:33340) is a protein-coding gene on chromosome 2p25.3, encoding Protein FAM110C (Q1W6H9). May play a role in microtubule organization.

Enables alpha-tubulin binding activity. Involved in positive regulation of cell migration; positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction; and regulation of cell projection assembly. Located in cell cortex.

Source: NCBI Gene 642273 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 83 total — 3 pathogenic
• MANE Select transcript: NM_001077710

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33340
Approved symbol	FAM110C
Name	family with sequence similarity 110 member C
Location	2p25.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184731
Ensembl biotype	protein_coding
OMIM	611395
Entrez	642273

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000327669, ENST00000460464, ENST00000461026

RefSeq mRNA: 1 — MANE Select: NM_001077710 NM_001077710

CCDS: CCDS42645

Canonical transcript exons

ENST00000327669 — 2 exons

Exon	Start	End
ENSE00001292553	45440	46505
ENSE00001537167	38814	41627

Expression profiles

Bgee: expression breadth ubiquitous, 213 present calls, max score 97.70.

FANTOM5 (CAGE): breadth broad, TPM avg 1.3292 / max 47.8406, expressed in 483 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26617	0.5470	329
26616	0.4823	272
26615	0.1552	81
26618	0.1109	49
26614	0.0338	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	97.70	gold quality
gingival epithelium	UBERON:0001949	97.14	gold quality
corpus epididymis	UBERON:0004359	96.78	gold quality
gingiva	UBERON:0001828	96.26	gold quality
epithelial cell of pancreas	CL:0000083	95.80	gold quality
germinal epithelium of ovary	UBERON:0001304	94.40	gold quality
esophagus squamous epithelium	UBERON:0006920	94.05	gold quality
lower esophagus mucosa	UBERON:0035834	93.98	gold quality
jejunal mucosa	UBERON:0000399	93.65	gold quality
seminal vesicle	UBERON:0000998	93.07	gold quality
esophagus mucosa	UBERON:0002469	92.98	gold quality
cauda epididymis	UBERON:0004360	92.89	gold quality
caput epididymis	UBERON:0004358	92.78	gold quality
palpebral conjunctiva	UBERON:0001812	92.22	gold quality
ileal mucosa	UBERON:0000331	91.00	gold quality
colonic mucosa	UBERON:0000317	90.02	gold quality
oral cavity	UBERON:0000167	89.97	gold quality
body of pancreas	UBERON:0001150	89.44	gold quality
mucosa of sigmoid colon	UBERON:0004993	89.41	gold quality
parietal pleura	UBERON:0002400	89.39	gold quality
oviduct epithelium	UBERON:0004804	88.49	gold quality
duodenum	UBERON:0002114	87.44	gold quality
endothelial cell	CL:0000115	87.26	gold quality
right lobe of liver	UBERON:0001114	87.01	gold quality
penis	UBERON:0000989	86.92	gold quality
metanephros cortex	UBERON:0010533	86.82	gold quality
rectum	UBERON:0001052	86.74	gold quality
pancreas	UBERON:0001264	86.22	gold quality
gall bladder	UBERON:0002110	86.18	gold quality
pericardium	UBERON:0002407	85.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PGR

miRNA regulators (miRDB)

110 targeting FAM110C, 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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-7-1-3P	99.91	71.53	4384

Literature-anchored findings (GeneRIF, showing 2)

• Ectopic eexpression impairs cell cycle progression through the G1 phase; overexpression induces aberrant microtubules. (PMID:17499476)
• Depletion of FAM110C by short interfering RNA reduced integrin-mediated filopodia formation, hepatocyte growth factor-induced migration, and phosphorylation of the Akt1 kinase in the epithelial cell line HepG2. (PMID:19698782)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam110c	ENSDARG00000096989
mus_musculus	Fam110c	ENSMUSG00000036136
rattus_norvegicus	Fam110c	ENSRNOG00000005660

Paralogs (3): FAM110A (ENSG00000125898), FAM110B (ENSG00000169122), FAM110D (ENSG00000197245)

Protein

Protein identifiers

Protein FAM110C — Q1W6H9 (reviewed: Q1W6H9)

All UniProt accessions (1): Q1W6H9

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in microtubule organization. May play a role in cell spreading and cell migration of epithelial cells; the function may involve the AKT1 signaling pathway.

Subunit / interactions. Interacts with AKT1; the interaction is transient and follows AKT1 activation. Interacts with PPP2CA and alpha-tubulin.

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

Tissue specificity. Detected in stomach, thyroid, trachea, adrenal gland and testis, and at low levels in prostate, ovary, intestine, colon, spinal cord and lymph node.

Similarity. Belongs to the FAM110 family.

RefSeq proteins (1): NP_001071178* (*=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 3, region of interest 2, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q1W6H9-F1	61.88	0.09

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): 241

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 121 (showing top): chr2p25, MENSE_HYPOXIA_UP, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, BILD_HRAS_ONCOGENIC_SIGNATURE, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, GOBP_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION, GOCC_CENTROSOME, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, GOBP_POSITIVE_REGULATION_OF_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION

GO Biological Process (3): positive regulation of cell migration (GO:0030335), positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051897), regulation of cell projection assembly (GO:0060491)

GO Molecular Function (2): alpha-tubulin binding (GO:0043014), protein binding (GO:0005515)

GO Cellular Component (7): spindle pole (GO:0000922), nucleus (GO:0005634), centrosome (GO:0005813), microtubule (GO:0005874), 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	2
cell migration	1
regulation of cell migration	1
positive regulation of cell motility	1
phosphatidylinositol 3-kinase/protein kinase B signal transduction	1
regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	1
positive regulation of intracellular signal transduction	1
cell projection assembly	1
regulation of cell projection organization	1
regulation of cellular component biogenesis	1
tubulin binding	1
binding	1
spindle	1
intracellular membrane-bounded organelle	1
centriole	1
microtubule organizing center	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
cytoplasm	1
cell periphery	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

336 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM110C	CSPP1	Q1MSJ5	942
FAM110C	SH3YL1	Q96HL8	542
FAM110C	ALKAL2	Q6UX46	541
FAM110C	TMEM47	Q9BQJ4	480
FAM110C	CNTN5	O94779	437
FAM110C	SNTG2	Q9NY99	430
FAM110C	CARMIL3	Q8ND23	421
FAM110C	Q3MI93	Q3MI93	418
FAM110C	COL11A1	P12107	409
FAM110C	AMN1	Q8IY45	396
FAM110C	ACMSD	Q8TDX5	380
FAM110C	TBX5	Q99593	378
FAM110C	MS4A13	Q5J8X5	370
FAM110C	LCP1	P13796	368
FAM110C	TMEM18	Q96B42	357

IntAct

16 interactions, top by confidence:

A	B	Type	Score
CSNK1E	PER2	psi-mi:“MI:0914”(association)	0.850
CSNK1E	FAM110C	psi-mi:“MI:0915”(physical association)	0.740
YWHAE	SRSF10	psi-mi:“MI:0914”(association)	0.560
Akt1	FAM110C	psi-mi:“MI:0915”(physical association)	0.540
FAM110C	Akt1	psi-mi:“MI:0914”(association)	0.540
FAM110C	Akt1	psi-mi:“MI:0403”(colocalization)	0.540
PDLIM7	ACTN4	psi-mi:“MI:0914”(association)	0.530
CSNK1E	ZSWIM8	psi-mi:“MI:0914”(association)	0.530
FAM110C	AKT1	psi-mi:“MI:0915”(physical association)	0.400
PDLIM7	CRYBG2	psi-mi:“MI:0914”(association)	0.350
CSNK1D	TMEM131L	psi-mi:“MI:0914”(association)	0.350
CAMK4	CNOT1	psi-mi:“MI:0914”(association)	0.350
CDH1	ESYT2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (18): FAM110C (Affinity Capture-RNA), FAM110C (Affinity Capture-Western), AKT1 (Affinity Capture-Western), TUBA1A (Affinity Capture-Western), FAM110C (Affinity Capture-Western), PPP2R4 (Affinity Capture-Western), FAM110C (Affinity Capture-Western), FAM110C (Proximity Label-MS), FAM110C (Proximity Label-MS), FAM110C (Affinity Capture-MS), FAM110C (Affinity Capture-MS), FAM110C (Affinity Capture-MS), FAM110C (Negative Genetic), FAM110C (Affinity Capture-MS), FAM110C (Affinity Capture-MS)

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	73
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
1315513	NM_001077710.3(FAM110C):c.691G>C (p.Ala231Pro)	Pathogenic
1315514	NM_001077710.3(FAM110C):c.690G>C (p.Glu230Asp)	Pathogenic
144454	GRCh38/hg38 2p25.3-25.2(chr2:30341-4932359)x3	Pathogenic

SpliceAI

358 predictions. Top by Δscore:

Variant	Effect	Δscore
2:42891:AAATT:A	donor_gain	0.9800
2:45435:CACA:C	donor_loss	0.9800
2:45436:ACACC:A	donor_loss	0.9800
2:45437:CACCT:C	donor_loss	0.9800
2:45438:AC:A	donor_loss	0.9800
2:45439:C:T	donor_loss	0.9800
2:45440:C:G	donor_loss	0.9500
2:45482:T:TA	donor_gain	0.9500
2:41625:TTCC:T	acceptor_loss	0.9400
2:41626:TCCTG:T	acceptor_loss	0.9400
2:41628:CTGAG:C	acceptor_loss	0.9400
2:41629:T:G	acceptor_loss	0.9400
2:41624:CTTC:C	acceptor_gain	0.9300
2:41628:C:CC	acceptor_gain	0.9300
2:41630:G:C	acceptor_loss	0.9200
2:42895:T:TA	donor_gain	0.9200
2:45434:ACAC:A	donor_loss	0.9000
2:45486:A:AC	donor_gain	0.9000
2:45487:C:CC	donor_gain	0.9000
2:41625:TTC:T	acceptor_gain	0.8400
2:45488:A:C	donor_gain	0.8400
2:45701:C:CT	donor_gain	0.8400
2:46247:A:AC	donor_gain	0.8300
2:46248:C:CC	donor_gain	0.8300
2:45702:C:CT	donor_gain	0.8200
2:41626:TC:T	acceptor_gain	0.8000
2:41627:CC:C	acceptor_gain	0.8000
2:45438:A:AC	donor_gain	0.7800
2:45439:C:CC	donor_gain	0.7800
2:44606:T:A	donor_gain	0.7600

AlphaMissense

2028 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:45498:C:A	W296C	0.998
2:45498:C:G	W296C	0.998
2:45500:A:G	W296R	0.998
2:45500:A:T	W296R	0.998
2:45505:A:T	I294N	0.997
2:45511:C:G	R292P	0.996
2:45515:C:G	A291P	0.996
2:45514:G:T	A291D	0.995
2:45505:A:G	I294T	0.994
2:45496:A:G	L297P	0.993
2:45505:A:C	I294S	0.993
2:45508:A:C	I293S	0.993
2:45516:G:C	N290K	0.993
2:45516:G:T	N290K	0.993
2:45517:T:A	N290I	0.993
2:45508:A:G	I293T	0.992
2:45512:G:T	R292S	0.991
2:45499:C:G	W296S	0.990
2:45732:G:C	F218L	0.990
2:45732:G:T	F218L	0.990
2:45734:A:G	F218L	0.990
2:46079:A:C	Y103D	0.990
2:45508:A:T	I293N	0.989
2:45518:T:C	N290D	0.989
2:45501:C:A	K295N	0.988
2:45501:C:G	K295N	0.988
2:45526:A:T	I287N	0.988
2:45729:G:C	F219L	0.988
2:45729:G:T	F219L	0.988
2:45731:A:G	F219L	0.988

dbSNP variants (sampled 300 via entrez): RS1000044716 (2:48034 G>A), RS1000087901 (2:38881 T>A,G), RS1000103119 (2:39517 G>A,C), RS1000564777 (2:43537 G>C), RS1000603237 (2:42262 AG>A), RS1000982983 (2:45145 A>C), RS1001625364 (2:47414 T>C), RS1001655480 (2:42271 T>C), RS1001892464 (2:44060 C>T), RS1001957273 (2:42600 C>A), RS1002041546 (2:43393 G>A), RS1002099676 (2:41955 A>G), RS1002469277 (2:43173 C>A), RS1002718166 (2:47101 G>A,C), RS1002767532 (2:46794 C>T)

Disease associations

OMIM: gene MIM:611395 | 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
GCST000905_7	Information processing speed	9.000000e-06
GCST010002_382	Refractive error	6.000000e-25

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004363	information processing speed

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	6
mercuric bromide	increases expression, affects cotreatment	2
entinostat	increases expression, affects cotreatment	2
Resveratrol	affects cotreatment, decreases expression	2
Benzo(a)pyrene	affects methylation, increases expression	2
Calcitriol	increases expression, affects cotreatment	2
Estradiol	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Cyclosporine	decreases expression, increases expression	2
Cadmium Chloride	decreases expression, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
beta-lapachone	increases expression	1
afimoxifene	decreases reaction, decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
cupric chloride	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
clothianidin	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Carbamazepine	affects expression	1
Coumestrol	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1

Clinical trials (associated diseases)

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