FAM117B

Summary

FAM117B (family with sequence similarity 117 member B, HGNC:14440) is a protein-coding gene on chromosome 2q33.2, encoding Protein FAM117B (Q6P1L5).

At a glance

• GWAS associations: 19
• Clinical variants (ClinVar): 96 total
• MANE Select transcript: NM_173511

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14440
Approved symbol	FAM117B
Name	family with sequence similarity 117 member B
Location	2q33.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38771
Ensembl gene	ENSG00000138439
Ensembl biotype	protein_coding
Entrez	150864

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron

ENST00000392238, ENST00000481658

RefSeq mRNA: 1 — MANE Select: NM_173511 NM_173511

CCDS: CCDS33362

Canonical transcript exons

ENST00000392238 — 8 exons

Exon	Start	End
ENSE00001130319	202759233	202759353
ENSE00001172613	202724917	202725009
ENSE00001279754	202757213	202757438
ENSE00001279764	202755538	202755681
ENSE00001279772	202726250	202726363
ENSE00001279804	202765446	202769757
ENSE00001661795	202634969	202635788
ENSE00003531015	202695881	202696032

Expression profiles

Bgee: expression breadth ubiquitous, 240 present calls, max score 95.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.0012 / max 217.0966, expressed in 1572 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
24727	11.4058	1562
24731	0.3709	114
24726	0.2149	52
24730	0.0095	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	95.46	gold quality
gingiva	UBERON:0001828	92.23	gold quality
gingival epithelium	UBERON:0001949	92.12	gold quality
ganglionic eminence	UBERON:0004023	90.73	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.60	gold quality
esophagus squamous epithelium	UBERON:0006920	87.06	gold quality
mucosa of sigmoid colon	UBERON:0004993	85.79	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.55	gold quality
secondary oocyte	CL:0000655	85.22	gold quality
epithelial cell of pancreas	CL:0000083	85.18	gold quality
colonic mucosa	UBERON:0000317	85.02	gold quality
ileal mucosa	UBERON:0000331	84.68	gold quality
oral cavity	UBERON:0000167	84.52	gold quality
skin of hip	UBERON:0001554	84.06	gold quality
ventricular zone	UBERON:0003053	83.44	gold quality
epithelium of nasopharynx	UBERON:0001951	82.79	gold quality
upper leg skin	UBERON:0004262	82.40	gold quality
oocyte	CL:0000023	82.38	gold quality
sperm	CL:0000019	81.82	silver quality
palpebral conjunctiva	UBERON:0001812	81.53	gold quality
oviduct epithelium	UBERON:0004804	81.21	gold quality
leukocyte	CL:0000738	81.03	gold quality
monocyte	CL:0000576	80.91	gold quality
thymus	UBERON:0002370	80.40	gold quality
right adrenal gland cortex	UBERON:0035827	80.15	gold quality
jejunal mucosa	UBERON:0000399	80.08	gold quality
middle temporal gyrus	UBERON:0002771	79.73	gold quality
Brodmann (1909) area 23	UBERON:0013554	79.37	gold quality
right adrenal gland	UBERON:0001233	79.06	gold quality
left adrenal gland	UBERON:0001234	78.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

265 targeting FAM117B, 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-6867-5P	100.00	82.21	3464
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-6740-5P	100.00	65.64	932
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-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4803	99.98	71.99	3117

Literature-anchored findings (GeneRIF, showing 1)

• FAM117B promotes gastric cancer growth and drug resistance by targeting the KEAP1/NRF2 signaling pathway. (PMID:36719368)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam117bb	ENSDARG00000009839
danio_rerio	fam117ba	ENSDARG00000074921
mus_musculus	Fam117b	ENSMUSG00000041040
rattus_norvegicus	Fam117b	ENSRNOG00000022066

Paralogs (2): GLCCI1 (ENSG00000106415), FAM117A (ENSG00000121104)

Protein

Protein identifiers

Protein FAM117B — Q6P1L5 (reviewed: Q6P1L5)

Alternative names: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 13 protein

All UniProt accessions (1): Q6P1L5

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. ALS2CR13 is mapped in the genomic region covering the complete candidate region for Amyotrophic lateral sclerosis 2 (ALS2).

Isoforms (2)

UniProt ID	Names	Canonical?
Q6P1L5-1	1	yes
Q6P1L5-2	2

RefSeq proteins (1): NP_775782* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026642	Glcci1/FAM117	Family

Pfam: PF15388

UniProt features (27 total): compositionally biased region 10, modified residue 10, region of interest 3, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P1L5-F1	53.34	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 (10): 10, 106, 210, 219, 220, 273, 345, 391, 449, 457

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 198 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GGGACCA_MIR133A_MIR133B, AAGCAAT_MIR137, PAX4_01, AREB6_03, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, HNF1_Q6, SP1_Q2_01, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN, E4F1_Q6, AAAGGGA_MIR204_MIR211, SOX5_01, CAGCTTT_MIR320, MZF1_02

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

520 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM117B	ICA1L	Q8NDH6	654
FAM117B	NBEAL1	Q6ZS30	652
FAM117B	RNF169	Q8NCN4	624
FAM117B	TROAP	Q12815	607
FAM117B	RAD54L2	Q9Y4B4	546
FAM117B	TRAF3	Q13114	538
FAM117B	FAM53C	Q9NYF3	518
FAM117B	EFCAB11	Q9BUY7	504
FAM117B	MCMBP	Q9BTE3	504
FAM117B	RBM43	Q6ZSC3	483
FAM117B	DCAF7	P61962	475
FAM117B	WDR12	Q9GZL7	447
FAM117B	AMER1	Q5JTC6	447
FAM117B	SLC25A44	Q96H78	445
FAM117B	SEC14L6	B5MCN3	417

IntAct

147 interactions, top by confidence:

A	B	Type	Score
DYNLL1	FAM117B	psi-mi:“MI:0915”(physical association)	0.920
FAM117B	DYNLL2	psi-mi:“MI:0915”(physical association)	0.880
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
FAM117B	DCAF7	psi-mi:“MI:0914”(association)	0.730
FAM117B	KEAP1	psi-mi:“MI:0915”(physical association)	0.720
KEAP1	FAM117B	psi-mi:“MI:0915”(physical association)	0.720
FAM117B	BANP	psi-mi:“MI:0915”(physical association)	0.670
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
PSMC3	PSMD12	psi-mi:“MI:0914”(association)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAE	RGS12	psi-mi:“MI:0914”(association)	0.610
YWHAB	BLTP3B	psi-mi:“MI:2364”(proximity)	0.610
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
BANP	FAM117B	psi-mi:“MI:0915”(physical association)	0.560
FAM117B	BANP	psi-mi:“MI:0915”(physical association)	0.560
AGR2	FAM117B	psi-mi:“MI:0915”(physical association)	0.560
FAM117B	ATP5PB	psi-mi:“MI:0915”(physical association)	0.560
DR1	FAM117B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (94): FAM117B (Two-hybrid), FAM117B (Two-hybrid), FAM117B (Affinity Capture-RNA), FAM117B (Affinity Capture-MS), FAM117B (Affinity Capture-MS), FAM117B (Two-hybrid), FAM117B (Affinity Capture-MS), TNKS (Affinity Capture-MS), DYRK1B (Affinity Capture-MS), IMMP1L (Affinity Capture-MS), TNKS2 (Affinity Capture-MS), DYRK1A (Affinity Capture-MS), TSC22D2 (Affinity Capture-MS), FAM117B (Affinity Capture-MS), FNTB (Affinity Capture-MS)

ESM2 similar proteins: A0A088MLT8, A6NNE9, A6P320, B3KU38, B5DF41, D4AE48, G3V9M2, O15079, O43521, O54918, O75081, O88498, P0C1G7, P0DPB3, P0DPB4, P49796, P53349, P78524, Q14DQ1, Q1LY51, Q3U3E2, Q50H33, Q5FVG6, Q5XKK7, Q60698, Q62925, Q68FF7, Q6P1L5, Q6ZNC4, Q7TNF9, Q80TE3, Q80U23, Q80U62, Q80UZ0, Q86VQ1, Q8BGW2, Q8BWU3, Q8CBH7, Q8IWP9, Q8K3I9

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 65 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 BAD and translocation to mitochondria	7	108.8×	3e-11
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	96.0×	4e-11
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	96.0×	4e-11
Activation of BH3-only proteins	7	70.9×	3e-10
Intrinsic Pathway for Apoptosis	8	47.8×	3e-10
RHO GTPases activate PKNs	7	45.3×	7e-09
FOXO-mediated transcription	5	34.3×	7e-06
Apoptosis	8	27.4×	2e-08

GO biological processes:

GO term	Partners	Fold	FDR
protein targeting	5	31.1×	2e-04
substantia nigra development	5	31.1×	2e-04
intracellular protein localization	7	12.4×	4e-04
proteasome-mediated ubiquitin-dependent protein catabolic process	8	7.1×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	77
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1516 predictions. Top by Δscore:

Variant	Effect	Δscore
2:202635784:AGCAG:A	donor_gain	1.0000
2:202635785:GCAG:G	donor_gain	1.0000
2:202635785:GCAGG:G	donor_gain	1.0000
2:202635786:CAG:C	donor_gain	1.0000
2:202635787:AGG:A	donor_loss	1.0000
2:202635789:G:GG	donor_gain	1.0000
2:202695873:A:AG	acceptor_gain	1.0000
2:202695874:A:G	acceptor_gain	1.0000
2:202695876:T:G	acceptor_gain	1.0000
2:202695877:CTAG:C	acceptor_loss	1.0000
2:202695878:TAG:T	acceptor_loss	1.0000
2:202695879:A:AG	acceptor_gain	1.0000
2:202695879:A:AT	acceptor_loss	1.0000
2:202695879:AG:A	acceptor_gain	1.0000
2:202695879:AGGT:A	acceptor_gain	1.0000
2:202695880:G:GT	acceptor_gain	1.0000
2:202695880:GG:G	acceptor_gain	1.0000
2:202695880:GGT:G	acceptor_gain	1.0000
2:202695880:GGTG:G	acceptor_gain	1.0000
2:202695880:GGTGA:G	acceptor_gain	1.0000
2:202696028:CACAG:C	donor_gain	1.0000
2:202696029:ACAG:A	donor_gain	1.0000
2:202696029:ACAGG:A	donor_loss	1.0000
2:202696030:CAG:C	donor_gain	1.0000
2:202696030:CAGG:C	donor_loss	1.0000
2:202696031:AG:A	donor_gain	1.0000
2:202696031:AGGTA:A	donor_loss	1.0000
2:202696032:GG:G	donor_gain	1.0000
2:202696032:GGTA:G	donor_loss	1.0000
2:202696033:G:C	donor_loss	1.0000

AlphaMissense

3808 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:202726260:T:C	L286S	1.000
2:202726262:C:A	R287S	1.000
2:202726263:G:C	R287P	1.000
2:202726272:T:C	L290S	1.000
2:202726283:A:G	K294E	1.000
2:202726285:A:C	K294N	1.000
2:202726285:A:T	K294N	1.000
2:202755623:T:C	L349S	1.000
2:202755632:A:T	E352V	1.000
2:202755635:T:A	I353N	1.000
2:202755635:T:G	I353S	1.000
2:202757232:G:A	G375D	1.000
2:202759275:C:A	P458Q	1.000
2:202759298:T:C	F466L	1.000
2:202759299:T:C	F466S	1.000
2:202759299:T:G	F466C	1.000
2:202759300:C:A	F466L	1.000
2:202759300:C:G	F466L	1.000
2:202759305:G:C	R468T	1.000
2:202759305:G:T	R468M	1.000
2:202759306:G:C	R468S	1.000
2:202759306:G:T	R468S	1.000
2:202759310:C:T	P470S	1.000
2:202759311:C:A	P470H	1.000
2:202759313:C:T	P471S	1.000
2:202759314:C:A	P471H	1.000
2:202759319:G:C	G473R	1.000
2:202759319:G:T	G473C	1.000
2:202759320:G:A	G473D	1.000
2:202759320:G:T	G473V	1.000

dbSNP variants (sampled 300 via entrez): RS1000003098 (2:202705310 GAAAAA>G,GAA,GAAAA,GAAAAAA), RS1000044919 (2:202737861 C>A,T), RS1000063948 (2:202732050 T>A,C), RS1000071354 (2:202661145 G>C,T), RS1000078355 (2:202658127 G>A), RS1000081515 (2:202754609 C>T), RS1000091738 (2:202686091 A>G), RS1000149063 (2:202639174 G>A), RS1000164187 (2:202725971 A>T), RS1000178019 (2:202706676 C>T), RS1000185425 (2:202767332 G>A), RS1000186517 (2:202760076 T>C), RS1000200313 (2:202638818 C>T), RS1000201880 (2:202723191 G>T), RS1000205662 (2:202668770 A>G)

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
GCST002221_48	Cholesterol, total	2.000000e-09
GCST002896_10	Cholesterol, total	5.000000e-09
GCST002898_13	LDL cholesterol	6.000000e-09
GCST004235_42	Total cholesterol levels	8.000000e-10
GCST005538_2	Sarcoidosis	2.000000e-08
GCST006614_65	Total cholesterol levels	2.000000e-27
GCST006947_39	Feeling fed-up	1.000000e-08
GCST010204_111	Low density lipoprotein cholesterol levels	1.000000e-24
GCST010241_91	Apolipoprotein A1 levels	5.000000e-13
GCST010242_418	HDL cholesterol levels	2.000000e-23
GCST010243_35	Apolipoprotein B levels	2.000000e-18
GCST010245_151	LDL cholesterol levels	9.000000e-18
GCST010698_18	Subcortical volume (min-P)	1.000000e-08
GCST010699_69	Brain morphology (min-P)	9.000000e-20
GCST010700_6	Cortical thickness (MOSTest)	2.000000e-14
GCST010701_36	Cortical surface area (MOSTest)	2.000000e-24
GCST010702_146	Subcortical volume (MOSTest)	2.000000e-13
GCST010703_42	Brain morphology (MOSTest)	1.000000e-08
GCST90002385_458	High light scatter reticulocyte count	5.000000e-12

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004574	total cholesterol measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0009588	feeling “fed-up” measurement
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004615	apolipoprotein B measurement
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	3
sodium arsenite	increases expression, decreases expression, increases abundance	2
Arsenic	affects expression, increases abundance, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
methylmercuric chloride	increases expression	1
nickel sulfate	increases expression	1
coumarin	increases phosphorylation	1
hydroquinone	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Allergens	increases expression, affects cotreatment, increases abundance	1
Vehicle Emissions	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression, increases abundance	1
Caffeine	increases phosphorylation	1
Cisplatin	decreases expression	1
Diethylhexyl Phthalate	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Oxygen	increases expression	1
Phthalic Acids	increases methylation	1
Quercetin	decreases expression	1
Thiram	decreases expression	1

Clinical trials (associated diseases)

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