FAM120C

Summary

FAM120C (family with sequence similarity 120 member C, HGNC:16949) is a protein-coding gene on chromosome Xp11.22, encoding Constitutive coactivator of PPAR-gamma-like protein 2 (Q9NX05).

This gene encodes a potential transmembrane protein and lies in a region where mutations and deletions have been associated with intellectual disability and autism. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 54954 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 205 total — 3 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_017848

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16949
Approved symbol	FAM120C
Name	family with sequence similarity 120 member C
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Aliases	ORF34, FLJ20506
Ensembl gene	ENSG00000184083
Ensembl biotype	protein_coding
OMIM	300741
Entrez	54954

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000328235, ENST00000375180, ENST00000477084, ENST00000497680

RefSeq mRNA: 3 — MANE Select: NM_017848 NM_001300788, NM_017848, NM_198456

CCDS: CCDS14356, CCDS55421, CCDS75987

Canonical transcript exons

ENST00000375180 — 16 exons

Exon	Start	End
ENSE00001295956	54091312	54091426
ENSE00001314426	54085715	54085916
ENSE00001316357	54087755	54087964
ENSE00001364079	54157689	54157771
ENSE00001365333	54135528	54135604
ENSE00001368219	54134831	54135111
ENSE00001369447	54133773	54134046
ENSE00001369586	54151245	54151373
ENSE00001369910	54159370	54159616
ENSE00001370367	54116545	54116794
ENSE00001370881	54136491	54136590
ENSE00001381626	54132692	54132863
ENSE00001466014	54068324	54073287
ENSE00003558903	54080232	54080289
ENSE00003591082	54081322	54081460
ENSE00003850750	54182500	54183254

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 90.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.1618 / max 165.0067, expressed in 1794 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199384	13.4778	1768
199385	4.6841	1430

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
inferior vagus X ganglion	UBERON:0005363	90.45	gold quality
ventral tegmental area	UBERON:0002691	88.85	gold quality
medial globus pallidus	UBERON:0002477	87.84	gold quality
subthalamic nucleus	UBERON:0001906	87.65	gold quality
globus pallidus	UBERON:0001875	87.48	gold quality
superior vestibular nucleus	UBERON:0007227	87.43	gold quality
substantia nigra pars reticulata	UBERON:0001966	85.56	gold quality
cerebellar vermis	UBERON:0004720	84.78	silver quality
mucosa of paranasal sinus	UBERON:0005030	84.28	gold quality
trigeminal ganglion	UBERON:0001675	84.23	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.76	gold quality
dorsal plus ventral thalamus	UBERON:0001897	83.29	gold quality
epithelium of nasopharynx	UBERON:0001951	82.65	gold quality
lateral globus pallidus	UBERON:0002476	82.51	gold quality
dorsal root ganglion	UBERON:0000044	82.47	gold quality
substantia nigra pars compacta	UBERON:0001965	82.46	gold quality
ventricular zone	UBERON:0003053	82.31	gold quality
corpus callosum	UBERON:0002336	82.30	gold quality
pons	UBERON:0000988	82.15	gold quality
germinal epithelium of ovary	UBERON:0001304	82.06	gold quality
pericardium	UBERON:0002407	81.73	silver quality
nipple	UBERON:0002030	81.41	gold quality
tendon of biceps brachii	UBERON:0008188	81.26	silver quality
oocyte	CL:0000023	80.96	gold quality
medulla oblongata	UBERON:0001896	80.72	gold quality
corpus epididymis	UBERON:0004359	80.57	gold quality
saphenous vein	UBERON:0007318	80.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.45	gold quality
caput epididymis	UBERON:0004358	80.39	gold quality
renal medulla	UBERON:0000362	79.99	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

191 targeting FAM120C, 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-8485	100.00	77.57	4731
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505

Literature-anchored findings (GeneRIF, showing 2)

• Xp11.22 deletion including genes PHF8, FAM120C and WNK3 may be involved in the pathogenesis of autism. (PMID:18498374)
• FAM120C is a novel candidate gene for autism spectrum disorder based on genetic evidence and the brain expression pattern. (PMID:25258334)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam120c	ENSDARG00000019205
mus_musculus	Fam120c	ENSMUSG00000025262
rattus_norvegicus	Fam120c	ENSRNOG00000062231

Paralogs (2): FAM120A (ENSG00000048828), FAM120B (ENSG00000112584)

Protein

Protein identifiers

Constitutive coactivator of PPAR-gamma-like protein 2 — Q9NX05 (reviewed: Q9NX05)

Alternative names: Protein FAM120C, Tumor antigen BJ-HCC-21

All UniProt accessions (2): Q9NX05, F8W881

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed at low levels in a number of tissues.

Similarity. Belongs to the constitutive coactivator of PPAR-gamma family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NX05-1	1	yes
Q9NX05-2	2

RefSeq proteins (3): NP_001287717, NP_060318, NP_940858 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026784	Coact_PPARg	Family
IPR029060	PIN-like_dom_sf	Homologous_superfamily

UniProt features (17 total): compositionally biased region 6, region of interest 3, modified residue 2, splice variant 2, sequence variant 2, chain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NX05-F1	69.02	0.44

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 (3): 58, 977, 1042

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): E2F_Q4_01, TGCGCANK_UNKNOWN, E2F_Q3, YY1_02, AAAGGGA_MIR204_MIR211, TGANTCA_AP1_C, GATA1_03, E2F1_Q3, CTTTGTA_MIR524, E2F_Q6_01, PARENT_MTOR_SIGNALING_UP, TGGAAA_NFAT_Q4_01, ACTWSNACTNY_UNKNOWN, GCCATNTTG_YY1_Q6, TCCCRNNRTGC_UNKNOWN

GO Biological Process (0):

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

702 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM120C	PHF8	Q9UPP1	851
FAM120C	WNK3	Q9BYP7	813
FAM120C	DNAJC28	Q9NX36	720
FAM120C	MPLKIP	Q8TAP9	719
FAM120C	A0A090J7P6	A0A090J7P6	715
FAM120C	ERCC5	P28715	668
FAM120C	SUGCT	Q9HAC7	608
FAM120C	CTTNBP2	Q8WZ74	593
FAM120C	TAX1BP1	Q86VP1	587
FAM120C	CWC15	Q9P013	571
FAM120C	EPAS1	Q99814	529
FAM120C	FAM3B	P58499	521
FAM120C	CENPVL1	A0A0U1RR11	480
FAM120C	ASZ1	Q8WWH4	479
FAM120C	PCBP1	Q15365	474

IntAct

22 interactions, top by confidence:

A	B	Type	Score
P4HA3	FAM171A2	psi-mi:“MI:0914”(association)	0.640
HNRNPC	CASC3	psi-mi:“MI:0914”(association)	0.530
TFCP2	FAM120C	psi-mi:“MI:0915”(physical association)	0.370
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
SEC16A	NCOR2	psi-mi:“MI:0914”(association)	0.350
HNRNPU		psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
HNRNPH1	VWA8	psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350
FAM120A	GTPBP10	psi-mi:“MI:0914”(association)	0.350
CCL3	KRBA1	psi-mi:“MI:0914”(association)	0.350
HNRNPC	APOBEC3DE	psi-mi:“MI:0914”(association)	0.350
PABPC5	APOBEC3DE	psi-mi:“MI:0914”(association)	0.350
YBX1	NOP56	psi-mi:“MI:0914”(association)	0.350
MYO6	GIPC1	psi-mi:“MI:2364”(proximity)	0.270
LIN28B	MEX3A	psi-mi:“MI:2364”(proximity)	0.270
SMNDC1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
SUMO1	CHD2	psi-mi:“MI:0914”(association)	0.000

BioGRID (210): BANP (Two-hybrid), FAM120C (Affinity Capture-MS), TFCP2 (Two-hybrid), FAM120C (Affinity Capture-MS), FAM120C (Affinity Capture-MS), FAM120C (Affinity Capture-MS), FAM120C (Affinity Capture-MS), FAM120C (Affinity Capture-MS), FAM120C (Affinity Capture-RNA), FAM120C (Proximity Label-MS), FAM120C (Affinity Capture-MS), FAM120C (Affinity Capture-MS), FAM120C (Proximity Label-MS), FAM120C (Proximity Label-MS), FAM120C (Affinity Capture-MS)

ESM2 similar proteins: A0JPH4, A2RSY1, A6H7H1, A6QNT4, B2RUR8, B5X165, D2HNW6, F1R7R1, O15550, O54828, O70546, O75916, O88974, P49140, P49805, P53349, P55265, P55266, Q13191, Q13233, Q15047, Q2YDD2, Q3KR73, Q3TTA7, Q5PQS6, Q5R6Y9, Q60698, Q62925, Q6A0A9, Q6DEZ2, Q6GQL0, Q6GQQ9, Q6NXD8, Q6RI63, Q80U62, Q86XL3, Q8C3F2, Q8K2L8, Q8K4S7, Q8N5Y2

Diamond homologs: A6H7H1, Q5T035, Q6A0A9, Q6DEZ2, Q8C3F2, Q96EK7, Q9NX05, Q9NZB2, A6QNT4, Q6RI63

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 34 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
Processing of Capped Intron-Containing Pre-mRNA	6	24.6×	2e-05
mRNA Polyadenylation	5	22.0×	2e-04
mRNA Splicing - Major Pathway	6	16.4×	1e-04
Dengue Virus-Host Interactions	5	11.4×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	65
Likely benign	6
Benign	2

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
2685088	GRCh37/hg19 Xp11.22(chrX:53954419-54291347)x0	Pathogenic
395687	GRCh37/hg19 Xp22.33-q28(chrX:70297-155255792)	Pathogenic
685927	GRCh37/hg19 Xp11.22(chrX:53384424-54103704)x2	Pathogenic
1526801	GRCh37/hg19 Xp11.22(chrX:53797930-54608609)	Likely pathogenic

SpliceAI

2768 predictions. Top by Δscore:

Variant	Effect	Δscore
X:54072997:C:A	donor_gain	1.0000
X:54073003:T:TA	donor_gain	1.0000
X:54080226:ACTT:A	donor_loss	1.0000
X:54080227:CTT:C	donor_loss	1.0000
X:54080228:TTA:T	donor_loss	1.0000
X:54080229:TA:T	donor_loss	1.0000
X:54080230:A:AC	donor_gain	1.0000
X:54080230:ACTT:A	donor_loss	1.0000
X:54080230:ACTTG:A	donor_gain	1.0000
X:54080231:C:CA	donor_gain	1.0000
X:54080231:CT:C	donor_gain	1.0000
X:54080231:CTT:C	donor_gain	1.0000
X:54080231:CTTG:C	donor_gain	1.0000
X:54080231:CTTGC:C	donor_gain	1.0000
X:54080299:G:GC	acceptor_gain	1.0000
X:54087734:AGCAG:A	donor_gain	1.0000
X:54087808:G:C	donor_gain	1.0000
X:54091307:CTCA:C	donor_loss	1.0000
X:54091308:TCA:T	donor_loss	1.0000
X:54091310:A:AC	donor_gain	1.0000
X:54091310:AC:A	donor_gain	1.0000
X:54091310:ACCTT:A	donor_loss	1.0000
X:54091311:C:CG	donor_loss	1.0000
X:54091311:C:CT	donor_gain	1.0000
X:54091311:CC:C	donor_gain	1.0000
X:54091311:CCT:C	donor_gain	1.0000
X:54091311:CCTT:C	donor_gain	1.0000
X:54091311:CCTTG:C	donor_gain	1.0000
X:54091422:TGTAC:T	acceptor_gain	1.0000
X:54091423:GTAC:G	acceptor_gain	1.0000

AlphaMissense

7091 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:54081396:C:A	W968C	1.000
X:54081396:C:G	W968C	1.000
X:54081398:A:G	W968R	1.000
X:54081398:A:T	W968R	1.000
X:54081427:A:G	L958P	1.000
X:54087844:A:G	W850R	1.000
X:54087844:A:T	W850R	1.000
X:54087862:A:G	W844R	1.000
X:54087862:A:T	W844R	1.000
X:54087867:A:T	V842D	1.000
X:54087876:C:A	G839V	1.000
X:54087876:C:T	G839D	1.000
X:54087877:C:G	G839R	1.000
X:54087878:A:C	C838W	1.000
X:54087879:C:T	C838Y	1.000
X:54087880:A:G	C838R	1.000
X:54087882:G:T	A837D	1.000
X:54087885:T:A	D836V	1.000
X:54087887:A:C	N835K	1.000
X:54087887:A:T	N835K	1.000
X:54087891:G:T	A834D	1.000
X:54087900:G:T	A831D	1.000
X:54087912:C:T	G827E	1.000
X:54116558:A:G	C767R	1.000
X:54116581:A:T	V759D	1.000
X:54116622:A:C	C745W	1.000
X:54116623:C:T	C745Y	1.000
X:54116624:A:G	C745R	1.000
X:54116629:A:G	L743P	1.000
X:54116632:A:G	F742S	1.000

dbSNP variants (sampled 300 via entrez): RS1000013251 (X:54162129 T>C), RS1000107714 (X:54176945 T>C), RS1000192837 (X:54109946 T>A), RS1000218077 (X:54128717 T>C), RS1000249354 (X:54128120 C>T), RS1000287648 (X:54093579 A>G), RS1000339751 (X:54182377 T>C), RS1000363880 (X:54104513 T>C), RS1000396452 (X:54103895 A>G), RS1000446354 (X:54161762 G>A), RS1000585095 (X:54126540 C>T), RS1000695911 (X:54101469 C>T), RS1000709699 (X:54180139 G>T), RS1000726684 (X:54101071 A>G), RS1000797899 (X:54111998 A>T)

Disease associations

OMIM: gene MIM:300741 | 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

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Tobacco Smoke Pollution	decreases expression	2
Aflatoxin B1	decreases methylation	2
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	affects methylation	1
potassium chromate(VI)	decreases expression	1
aflatoxin B2	increases methylation	1
nickel sulfate	increases expression	1
dinophysistoxin 1	decreases expression	1
abrine	decreases expression	1
NSC 689534	affects binding, decreases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Copper	affects binding, decreases expression	1
Ivermectin	decreases expression	1
Lead	decreases expression	1
Methapyrilene	affects methylation	1
Quercetin	increases expression	1
Ribonucleotides	affects binding	1
Valproic Acid	increases methylation	1
Zinc	increases expression	1
Cyclosporine	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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