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 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 82 total — 1 pathogenic
• GTEx eGene: eQTL in 16 tissues, sQTL in 1 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.94 (unconstrained)
• MANE Select transcript: NM_001077710
• Notable: 82 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

MANE Select: ENST00000327669

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 3: 1

ENST00000327669, ENST00000460464, ENST00000461026, ENST00001121672, ENST00001129227, ENST00001144741

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.

Highest expression (Bgee): pancreatic ductal cell, gingival epithelium, corpus epididymis, gingiva, epithelial cell of pancreas.

Genetic regulation across tissues (GTEx eQTL / sQTL)

FAM110C is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 16 tissues and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

17 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Skin Sun Exposed Lower leg	eqtl	6.0e-13	+0.75	2:38021:C:T
Skin Not Sun Exposed Suprapubic	eqtl	1.9e-08	+0.65	2:38021:C:T
Brain Frontal Cortex BA9	eqtl	2.4e-05	+0.26	2:30762:A:G
Brain Nucleus accumbens basal ganglia	eqtl	9.4e-05	+0.44	2:29443:T:C
Nerve Tibial	eqtl	1.6e-04	-0.85	2:38021:C:T
Thyroid	eqtl	1.6e-03	-0.39	2:46507:C:T
Esophagus Mucosa	eqtl	2.2e-03	-0.39	2:38021:C:T
Whole Blood	eqtl	2.4e-03	+0.31	2:28780:G:A
Brain Anterior cingulate cortex BA24	eqtl	2.5e-03	+0.38	2:67535:G:GT
Spleen	eqtl	4.1e-03	-1.35	2:176618:A:C
Lung	eqtl	6.5e-03	-0.32	2:25806:G:T
Brain Cortex	eqtl	7.1e-03	-0.20	2:69431:C:T
Artery Tibial	eqtl	1.0e-02	+0.14	2:30762:A:G
Pituitary	eqtl	2.0e-02	+0.35	2:41366:C:T
Colon Transverse	eqtl	2.8e-02	+0.49	2:389102:A:G
Heart Left Ventricle	eqtl	4.0e-02	-0.21	2:131828:G:A
Adrenal Gland	sqtl	4.8e-02	-0.33	2:907897:C:T

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

showing 100 of 253 tissues 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
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.37	gold quality
mammalian vulva	UBERON:0000997	85.34	gold quality
upper leg skin	UBERON:0004262	85.34	gold quality
kidney epithelium	UBERON:0004819	85.12	gold quality
pharyngeal mucosa	UBERON:0000355	84.93	gold quality
liver	UBERON:0002107	84.49	gold quality
fallopian tube	UBERON:0003889	84.43	gold quality
endometrium	UBERON:0001295	84.31	gold quality
cardiac muscle of right atrium	UBERON:0003379	84.14	silver quality
vagina	UBERON:0000996	83.75	gold quality
mucosa of transverse colon	UBERON:0004991	83.67	gold quality
decidua	UBERON:0002450	83.11	gold quality
adult mammalian kidney	UBERON:0000082	83.09	gold quality
left ventricle myocardium	UBERON:0006566	82.21	gold quality
zone of skin	UBERON:0000014	81.80	gold quality
skin of leg	UBERON:0001511	81.73	gold quality
kidney	UBERON:0002113	81.51	gold quality
right uterine tube	UBERON:0001302	81.12	gold quality
metanephros	UBERON:0000081	81.10	gold quality
skin of abdomen	UBERON:0001416	80.99	gold quality
upper arm skin	UBERON:0004263	80.96	gold quality
islet of Langerhans	UBERON:0000006	80.78	gold quality
adrenal tissue	UBERON:0018303	80.38	gold quality
mouth mucosa	UBERON:0003729	79.16	gold quality
left uterine tube	UBERON:0001303	79.12	gold quality
urinary bladder	UBERON:0001255	78.57	gold quality
left ovary	UBERON:0002119	78.46	gold quality
skin of hip	UBERON:0001554	78.39	gold quality
ovary	UBERON:0000992	78.36	gold quality
cortex of kidney	UBERON:0001225	78.04	gold quality
esophagus	UBERON:0001043	78.03	gold quality
peritoneum	UBERON:0002358	77.76	gold quality
omental fat pad	UBERON:0010414	77.74	gold quality
thyroid gland	UBERON:0002046	77.65	gold quality
left lobe of thyroid gland	UBERON:0001120	77.57	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	77.37	gold quality
minor salivary gland	UBERON:0001830	77.15	gold quality
transverse colon	UBERON:0001157	77.07	gold quality
nasal cavity epithelium	UBERON:0005384	76.08	silver quality
female reproductive system	UBERON:0000474	76.03	gold quality
tonsil	UBERON:0002372	75.86	gold quality
right lobe of thyroid gland	UBERON:0001119	75.82	gold quality
adipose tissue of abdominal region	UBERON:0007808	75.75	gold quality
saliva-secreting gland	UBERON:0001044	75.60	gold quality
pigmented layer of retina	UBERON:0001782	75.33	gold quality
left adrenal gland	UBERON:0001234	75.30	gold quality
parotid gland	UBERON:0001831	75.26	gold quality
left adrenal gland cortex	UBERON:0035825	75.10	gold quality
body of tongue	UBERON:0011876	75.08	gold quality
uterus	UBERON:0000995	75.03	gold quality
visceral pleura	UBERON:0002401	74.98	gold quality
right adrenal gland cortex	UBERON:0035827	74.90	gold quality
right adrenal gland	UBERON:0001233	74.45	gold quality
body of stomach	UBERON:0001161	74.33	gold quality
epithelium of nasopharynx	UBERON:0001951	74.29	gold quality
adrenal gland	UBERON:0002369	74.01	gold quality
jejunum	UBERON:0002115	73.90	gold quality
adrenal cortex	UBERON:0001235	73.87	gold quality
nasal cavity mucosa	UBERON:0001826	73.82	gold quality
small intestine	UBERON:0002108	73.75	gold quality
colonic epithelium	UBERON:0000397	73.65	gold quality
cardiac atrium	UBERON:0002081	73.18	gold quality
middle temporal gyrus	UBERON:0002771	72.94	gold quality
right atrium auricular region	UBERON:0006631	72.81	gold quality
Brodmann (1909) area 23	UBERON:0013554	72.80	gold quality
small intestine Peyer’s patch	UBERON:0003454	72.59	gold quality
stomach	UBERON:0000945	72.58	gold quality
adenohypophysis	UBERON:0002196	72.44	gold quality
mucosa of paranasal sinus	UBERON:0005030	72.38	gold quality
right ovary	UBERON:0002118	72.37	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

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 77 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Epididymis	tissue	19.5	medium
Seminal vesicle	tissue	18.6	low
Esophagus	tissue	16.7	medium
Liver	tissue	15.2	low
Vagina	tissue	15.0	medium
Urinary bladder	tissue	10.3	not detected
Duodenum	tissue	10.3	low
Pancreas	tissue	9.6	high
Rectum	tissue	9.5	low
Choroid plexus	tissue	9.2
Skin 1	tissue	9.1	high
Small intestine	tissue	9.1	low
Kidney	tissue	8.7	not detected
Fallopian tube	tissue	8.2	low
Colon	tissue	7.9	medium
Gallbladder	tissue	7.9	medium
Stomach 1	tissue	7.1	low
Ovary	tissue	5.9	medium
Cervix	tissue	5.5	medium
Thyroid gland	tissue	5.4	medium
Parathyroid gland	tissue	5.0	not detected
Breast	tissue	4.9	low
Hippocampus	tissue	4.1	medium
Pituitary gland	tissue	3.7
Endometrium 1	tissue	3.5	not detected
Testis	tissue	3.4	low
Nucleus accumbens	tissue	3.3
Basal ganglia	tissue	2.9	medium
Adrenal gland	tissue	2.9	medium
Postcentral gyrus	tissue	2.9
Olfactory bulb	tissue	2.9
Heart muscle	tissue	2.6	not detected
Cerebellum	tissue	2.5	medium
Lung	tissue	2.4	medium
Locus coeruleus	tissue	2.4
Hippocampal formation	tissue	2.4
Salivary gland	tissue	2.3	medium
Putamen	tissue	2.3
Ventral forebrain	tissue	2.3
Cerebral cortex	tissue	2.2	medium
Amygdala	tissue	2.2
Retrosplenial cortex	tissue	2.2
Retrosplenial and cingulate cortex	tissue	2.1
Temporal cortex	tissue	2.1
Insular cortex	tissue	2.1
Tonsil	tissue	2.0	low
Septum	tissue	2.0
Prostate	tissue	1.9	low
Entorhinal cortex	tissue	1.9
Occipital cortex	tissue	1.9
Corpus callosum	tissue	1.8
Prefrontal cortex	tissue	1.7
Smooth muscle	tissue	1.7	low
Thymus	tissue	1.7
Periaqueductal gray	tissue	1.7
Appendix	tissue	1.7	medium
Motor cortex	tissue	1.6
Superior colliculi	tissue	1.6
Somatosensory cortex	tissue	1.6
Medulla oblongata	tissue	1.5

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Nucleus of the diagonal band (9.1), Septal nuclei (8.4), Perirhinal gyrus (7.6), Olfactory area (7.5), Stria terminalis, bed nucleus (6.6).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PGR

miRNA regulators (miRDB)

Targeting FAM110C by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 110 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 7.58e-10, LOEUF 1.94, missense Z -3.28 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000327669 — one region, missense o/e 1.10.

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)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Pongo abelii	Q5R5R3	99.7%	Diamond
Bos taurus	A6H7I7	88.6%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
SH3YL1	protein-coding	26751
ACP1	protein-coding	52
ALKAL2	protein-coding	285016

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

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH uncertain

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)

Type	Positions
Phosphoserine	241

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

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 (6): spindle pole (GO:0000922), nucleus (GO:0005634), centrosome (GO:0005813), microtubule (GO:0005874), cell cortex (GO:0005938), cytoskeleton (GO:0005856)

GO top-level categories

21 GO namespaces:

Category	Terms
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
cellular anatomical structure	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 membraneless organelle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 5 of 11 annotations. The rest are phylogenetic / computational / electronic (IEA).

5 experimentally-supported GO terms:

GO term	NS	Evidence
positive regulation of cell migration	BP	mutant phenotype
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	BP	mutant phenotype
regulation of cell projection assembly	BP	mutant phenotype
cell cortex	CC	direct assay
alpha-tubulin binding	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 298 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM110C	CSPP1	Q1MSJ5	940
FAM110C	ALKAL2	Q6UX46	539
FAM110C	SH3YL1	Q96HL8	500
FAM110C	TMEM47	Q9BQJ4	454
FAM110C	RASSF9	O75901	409
FAM110C	APC2	O95996	404
FAM110C	CARMIL3	Q8ND23	395
FAM110C	PLEKHM3	Q6ZWE6	394
FAM110C	ST8SIA6	P61647	393
FAM110C	SNTG2	Q9NY99	370
FAM110C	CNTN5	O94779	366
FAM110C	RASSF6	Q6ZTQ3	366
FAM110C	Q3MI93	Q3MI93	359
FAM110C	WDFY2	Q96P53	350
FAM110C	UBXN6	Q9BZV1	349

IntAct

Human interaction partners of FAM110C in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

Partner	Interaction type	MIscore	Records
CSNK1E	physical association	0.740	1
AKT1	physical association	0.400	2

BioGRID (18 interactions; top human partners by supporting records): CSNK1E (Affinity Capture-MS; 4 records), AKT1 (Affinity Capture-Western; 2 records), PPP2R4 (Affinity Capture-Western; 2 records), TUBA1A (Affinity Capture-Western; 2 records), CAMK4 (Affinity Capture-MS), CDH1 (Proximity Label-MS), CIT (Affinity Capture-MS), CSNK1D (Affinity Capture-MS), HRAS (Proximity Label-MS), SHMT2 (Affinity Capture-RNA), VHL (Negative Genetic), YWHAE (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for FAM110C: 82 ClinVar records (1 pathogenic / likely pathogenic); 2 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	74
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
144454	GRCh38/hg38 2p25.3-25.2(chr2:30341-4932359)x3	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore FAM110C’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 19 predictions of 213):

Position(s)	Effect	Δscore	Sites
2:45438–45439	donor_loss	0.9800	5
2:45438	donor_loss	0.9700
2:45440	donor_loss	0.9500
2:41628–41629	acceptor_loss	0.9400	6
2:45482	donor_gain	0.9300
2:41630	acceptor_loss	0.9200
2:41636	acceptor_loss	0.8900
2:45440	donor_loss	0.8600
2:45440	donor_loss	0.8500
2:45488	donor_gain	0.8300

AlphaMissense

410 missense substitutions predicted likely pathogenic (of 2,028 scored), across 97 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
N290	8	0.983	0.993
D98	8	0.968	0.986
F219	8	0.948	0.988
F218	8	0.909	0.990
F237	8	0.895	0.978
D203	8	0.815	0.881
D43	8	0.805	0.906
F127	8	0.730	0.863
W296	7	0.989	0.998
C222	7	0.945	0.985
E288	7	0.935	0.985
C300	7	0.929	0.970
I294	7	0.913	0.997
F260	7	0.807	0.975
K106	6	0.953	0.980
R292	6	0.938	0.996
I293	6	0.935	0.993
K295	6	0.933	0.988
R96	6	0.932	0.985
R289	6	0.932	0.981

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

4 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	5.66e-08
Glioblastoma Multiforme (TCGA)	unfavorable	0.000218
Liver Hepatocellular Carcinoma (validation)	favorable	0.000292
Glioblastoma Multiforme (validation)	unfavorable	0.000446

Disease associations

OMIM: gene MIM:611395 | disease phenotypes:

GWAS associations

2 associations:

Study	Trait	p-value
GCST010002_39	Refractive error	6e-25
GCST000905_7	Information processing speed	9e-6

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0004363	information processing speed

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects cotreatment, increases expression, affects expression	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	increases expression, affects cotreatment	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
beta-lapachone	increases expression	1
afimoxifene	decreases expression, decreases reaction	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)

Via MONDO — disease-level, not drug-specific.