FAM117A

Summary

FAM117A (family with sequence similarity 117 member A, HGNC:24179) is a protein-coding gene on chromosome 17q21.33, encoding Protein FAM117A (Q9C073).

At a glance

• GWAS associations: 19
• Clinical variants (ClinVar): 70 total
• MANE Select transcript: NM_030802

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24179
Approved symbol	FAM117A
Name	family with sequence similarity 117 member A
Location	17q21.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000121104
Ensembl biotype	protein_coding
Entrez	81558

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 protein_coding_CDS_not_defined, 4 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000240364, ENST00000503573, ENST00000503720, ENST00000503855, ENST00000505159, ENST00000506156, ENST00000509347, ENST00000511743, ENST00000513602, ENST00000514018, ENST00000514841, ENST00000515240

RefSeq mRNA: 2 — MANE Select: NM_030802 NM_001411126, NM_030802

CCDS: CCDS11553, CCDS92358

Canonical transcript exons

ENST00000240364 — 8 exons

Exon	Start	End
ENSE00001109518	49710332	49711555
ENSE00002087402	49763892	49764131
ENSE00003474007	49717513	49717714
ENSE00003481546	49732551	49732720
ENSE00003548533	49716165	49716315
ENSE00003575856	49719760	49719894
ENSE00003586395	49720326	49720436
ENSE00003668955	49722499	49722594

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 98.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.7671 / max 1732.5700, expressed in 1725 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
166827	24.1119	1702
166830	0.2919	92
166825	0.1194	46
166828	0.1170	48
166831	0.0549	13
166832	0.0453	14
166833	0.0267	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
trabecular bone tissue	UBERON:0002483	98.27	gold quality
secondary oocyte	CL:0000655	95.35	gold quality
blood	UBERON:0000178	94.67	gold quality
oocyte	CL:0000023	94.46	gold quality
bone marrow	UBERON:0002371	94.40	gold quality
granulocyte	CL:0000094	94.31	gold quality
bone marrow cell	CL:0002092	93.94	gold quality
spleen	UBERON:0002106	90.39	gold quality
superficial temporal artery	UBERON:0001614	90.02	gold quality
upper leg skin	UBERON:0004262	90.02	gold quality
lymph node	UBERON:0000029	88.69	gold quality
right coronary artery	UBERON:0001625	88.62	gold quality
skin of hip	UBERON:0001554	88.53	gold quality
leukocyte	CL:0000738	88.15	gold quality
popliteal artery	UBERON:0002250	87.83	gold quality
tibial artery	UBERON:0007610	87.81	gold quality
thymus	UBERON:0002370	87.71	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.68	gold quality
mononuclear cell	CL:0000842	87.61	gold quality
neuron projection bundle connecting eye with brain	UBERON:0004904	87.50	gold quality
monocyte	CL:0000576	87.34	gold quality
body of uterus	UBERON:0009853	86.88	gold quality
pigmented layer of retina	UBERON:0001782	86.86	gold quality
retina	UBERON:0000966	86.84	gold quality
muscle layer of sigmoid colon	UBERON:0035805	86.63	gold quality
choroid plexus epithelium	UBERON:0003911	86.53	gold quality
vermiform appendix	UBERON:0001154	86.49	gold quality
aorta	UBERON:0000947	86.17	gold quality
right ovary	UBERON:0002118	86.09	gold quality
right uterine tube	UBERON:0001302	86.03	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	269.19
E-ANND-3	yes	9.82
E-MTAB-6386	no	190.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

121 targeting FAM117A, 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-4533	100.00	69.48	2758
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam117aa	ENSDARG00000078640
danio_rerio	fam117ab	ENSDARG00000079252
mus_musculus	Fam117a	ENSMUSG00000038893
rattus_norvegicus	Fam117a	ENSRNOG00000004417

Paralogs (2): GLCCI1 (ENSG00000106415), FAM117B (ENSG00000138439)

Protein

Protein identifiers

Protein FAM117A — Q9C073 (reviewed: Q9C073)

Alternative names: C/EBP-induced protein

All UniProt accessions (4): D6RFX7, D6RJ87, K7ENS5, Q9C073

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM117 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9C073-1	1	yes
Q9C073-2	2

RefSeq proteins (2): NP_001398055, NP_110429* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026642	Glcci1/FAM117	Family

Pfam: PF15388

UniProt features (22 total): modified residue 12, region of interest 4, compositionally biased region 3, chain 1, splice variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9C073-F1	56.34	0.02

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 (12): 67, 178, 193, 201, 213, 299, 319, 327, 354, 413, 428, 29

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 303 (showing top): CREL_01, LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_UP, RACCACAR_AML_Q6, ATGTTAA_MIR302C, NFKB_Q6, GTGCCTT_MIR506, NFKB_C, OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP, AML_Q6, AAAGACA_MIR511, GGGNNTTTCC_NFKB_Q6_01, TGANTCA_AP1_C, GATA1_04, GATA1_03, USF_02

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

284 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM117A	RNF169	Q8NCN4	541
FAM117A	LZTS2	Q9BRK4	532
FAM117A	BSDC1	Q9NW68	432
FAM117A	OR2V2	Q96R30	424
FAM117A	DLX3	O60479	408
FAM117A	DYRK1A	Q13627	402
FAM117A	SLC46A3	Q7Z3Q1	385
FAM117A	INPP5J	Q15735	375
FAM117A	TSSK6	Q9BXA6	365
FAM117A	LRFN2	Q9ULH4	365
FAM117A	TMEM185A	Q8NFB2	354
FAM117A	MACO1	Q8N5G2	352
FAM117A	SNF8	Q96H20	350
FAM117A	SIDT2	Q8NBJ9	345
FAM117A	TROAP	Q12815	336

IntAct

26 interactions, top by confidence:

A	B	Type	Score
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAG	SHTN1	psi-mi:“MI:0914”(association)	0.560
PICK1	ILVBL	psi-mi:“MI:0914”(association)	0.530
YWHAQ	IGLC7	psi-mi:“MI:0914”(association)	0.530
YWHAB	SHTN1	psi-mi:“MI:0914”(association)	0.530
ZAR1L	BCL2L11	psi-mi:“MI:0914”(association)	0.530
DYRK1B	BMAL1	psi-mi:“MI:0914”(association)	0.530
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
YWHAG	C1orf226	psi-mi:“MI:0914”(association)	0.350
DYRK1B	POM121C	psi-mi:“MI:0914”(association)	0.350
YWHAH	SHTN1	psi-mi:“MI:0914”(association)	0.350
YWHAQ	SHTN1	psi-mi:“MI:0914”(association)	0.350
YWHAB	FOXO6	psi-mi:“MI:0914”(association)	0.350
YWHAG	FOXO6	psi-mi:“MI:0914”(association)	0.350
YWHAQ	FOXO6	psi-mi:“MI:0914”(association)	0.350
YWHAH	FOXO6	psi-mi:“MI:0914”(association)	0.350
AKR7L	KIF2A	psi-mi:“MI:0914”(association)	0.350
DYRK1A	SIPA1L1	psi-mi:“MI:0914”(association)	0.350
FAM117A	COBLL1	psi-mi:“MI:0915”(physical association)	0.000
FAM117A	HMBOX1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (27): FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), HMBOX1 (Affinity Capture-MS), COBLL1 (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (Affinity Capture-MS), FAM117A (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: Q3U3E2, Q6P1L5, Q7TNF9, Q86VQ1, Q8K3I9, Q9C073

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 25 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
Activation of BH3-only proteins	5	137.9×	3e-08
Intrinsic Pathway for Apoptosis	5	81.3×	1e-07
Apoptosis	5	46.6×	1e-06
Programmed Cell Death	5	40.7×	2e-06
Cell Cycle Checkpoints	5	24.6×	2e-05
RHO GTPase Effectors	5	18.9×	6e-05
Signaling by Rho GTPases	6	11.4×	9e-05
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	6	11.2×	9e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1460 predictions. Top by Δscore:

Variant	Effect	Δscore
17:49716156:TGTAC:T	donor_loss	1.0000
17:49716158:TACT:T	donor_loss	1.0000
17:49716159:ACTC:A	donor_loss	1.0000
17:49716160:CT:C	donor_loss	1.0000
17:49716161:T:TA	donor_loss	1.0000
17:49716162:CAC:C	donor_loss	1.0000
17:49716163:A:AC	donor_gain	1.0000
17:49716163:A:AT	donor_loss	1.0000
17:49716164:C:CT	donor_gain	1.0000
17:49716164:CG:C	donor_gain	1.0000
17:49716164:CGTGG:C	donor_gain	1.0000
17:49717507:GCTTA:G	donor_loss	1.0000
17:49717508:CTTAC:C	donor_loss	1.0000
17:49717509:TTAC:T	donor_loss	1.0000
17:49717510:TACCT:T	donor_loss	1.0000
17:49717512:C:CG	donor_loss	1.0000
17:49717714:TCTAA:T	acceptor_loss	1.0000
17:49717715:C:CC	acceptor_gain	1.0000
17:49717715:CTAAC:C	acceptor_loss	1.0000
17:49717716:T:C	acceptor_loss	1.0000
17:49719758:AC:A	donor_gain	1.0000
17:49719759:CC:C	donor_gain	1.0000
17:49719892:CGC:C	acceptor_gain	1.0000
17:49720324:AC:A	donor_gain	1.0000
17:49720325:CC:C	donor_gain	1.0000
17:49720446:C:CT	acceptor_gain	1.0000
17:49720446:C:T	acceptor_gain	1.0000
17:49720447:A:T	acceptor_gain	1.0000
17:49788845:GGAAG:G	donor_gain	1.0000
17:49788846:GAAGG:G	donor_gain	1.0000

AlphaMissense

2901 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:49711474:G:C	F381L	0.998
17:49711474:G:T	F381L	0.998
17:49711476:A:G	F381L	0.998
17:49720426:A:G	L158S	0.996
17:49732607:A:G	W104R	0.996
17:49732607:A:T	W104R	0.996
17:49719793:A:C	F225L	0.995
17:49719793:A:T	F225L	0.995
17:49719795:A:G	F225L	0.995
17:49719806:A:G	L221P	0.995
17:49732605:C:A	W104C	0.995
17:49732605:C:G	W104C	0.995
17:49711496:A:G	F374S	0.994
17:49720422:C:A	K159N	0.994
17:49720422:C:G	K159N	0.994
17:49711475:A:G	F381S	0.993
17:49716213:C:G	R338P	0.993
17:49719794:A:G	F225S	0.993
17:49720414:A:G	L162P	0.993
17:49711475:A:C	F381C	0.992
17:49716219:A:G	F336S	0.992
17:49711495:G:C	F374L	0.991
17:49711495:G:T	F374L	0.991
17:49711497:A:G	F374L	0.991
17:49711504:T:A	K371N	0.991
17:49711504:T:G	K371N	0.991
17:49716199:C:G	G343R	0.991
17:49716194:A:C	C344W	0.990
17:49716196:A:G	C344R	0.990
17:49711502:A:T	V372D	0.989

dbSNP variants (sampled 300 via entrez): RS1000032162 (17:49768529 A>T), RS1000075035 (17:49757277 G>T), RS1000124338 (17:49727243 T>C), RS1000149752 (17:49768789 C>T), RS1000163076 (17:49715210 CAAT>C), RS1000206834 (17:49775870 T>C), RS1000240856 (17:49726851 A>G), RS1000253087 (17:49768987 G>A), RS1000284438 (17:49761617 C>G), RS1000294228 (17:49783113 A>C), RS1000401922 (17:49734496 G>C), RS1000409348 (17:49741750 C>G,T), RS1000419948 (17:49782600 G>A), RS1000423927 (17:49782238 G>A,T), RS1000431021 (17:49728719 C>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

19 associations (top):

Study	Trait	p-value
GCST002788_1	Milk allergy	1.000000e-06
GCST004601_149	Red blood cell count	3.000000e-10
GCST009066_45	Mosaic loss of chromosome Y (Y chromosome dosage)	3.000000e-21
GCST009067_35	Mosaic loss of chromosome Y (Y chromosome dosage)	1.000000e-38
GCST009375_17	Mosaic loss of chromosome Y (Y chromosome dosage)	9.000000e-10
GCST90002390_116	Mean corpuscular hemoglobin	2.000000e-48
GCST90002390_117	Mean corpuscular hemoglobin	3.000000e-15
GCST90002392_20	Mean corpuscular volume	2.000000e-62
GCST90002392_21	Mean corpuscular volume	4.000000e-23
GCST90002392_297	Mean corpuscular volume	2.000000e-10
GCST90002392_298	Mean corpuscular volume	1.000000e-09
GCST90002396_663	Mean reticulocyte volume	8.000000e-10
GCST90002396_664	Mean reticulocyte volume	4.000000e-70
GCST90002396_665	Mean reticulocyte volume	9.000000e-38
GCST90002397_577	Mean spheric corpuscular volume	4.000000e-69
GCST90002397_578	Mean spheric corpuscular volume	2.000000e-32
GCST90002403_362	Red blood cell count	4.000000e-18
GCST90002404_168	Red cell distribution width	3.000000e-10
GCST90002404_169	Red cell distribution width	1.000000e-10

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0007019	milk allergy measurement
EFO:0004305	erythrocyte count
EFO:0007783	mosaic loss of chromosome Y measurement
EFO:0004527	mean corpuscular hemoglobin
EFO:0010701	mean reticulocyte volume
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression, affects expression, increases expression	5
Benzo(a)pyrene	decreases expression	4
Tetrachlorodibenzodioxin	decreases expression, affects expression	3
Valproic Acid	affects expression, decreases methylation, increases expression	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Silicon Dioxide	decreases expression, increases expression	2
Cyclosporine	decreases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
afuresertib	increases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
scriptaid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
licochalcone B	increases expression	1
jinfukang	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Docetaxel	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Air Pollutants, Occupational	affects expression	1
Caffeine	affects phosphorylation	1

Clinical trials (associated diseases)

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