FAM43B

Summary

FAM43B (family with sequence similarity 43 member B, HGNC:31791) is a protein-coding gene on chromosome 1p36.12, encoding Protein FAM43B (Q6ZT52).

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_207334

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31791
Approved symbol	FAM43B
Name	family with sequence similarity 43 member B
Location	1p36.12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ44952
Ensembl gene	ENSG00000183114
Ensembl biotype	protein_coding
Entrez	163933

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000332947

RefSeq mRNA: 1 — MANE Select: NM_207334 NM_207334

CCDS: CCDS209

Canonical transcript exons

ENST00000332947 — 1 exons

Exon	Start	End
ENSE00001311821	20552573	20555020

Expression profiles

Bgee: expression breadth ubiquitous, 154 present calls, max score 86.98.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5656 / max 64.8391, expressed in 442 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1121	1.5656	442

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right adrenal gland cortex	UBERON:0035827	86.98	gold quality
right adrenal gland	UBERON:0001233	86.79	gold quality
left adrenal gland cortex	UBERON:0035825	86.39	gold quality
left adrenal gland	UBERON:0001234	86.21	gold quality
adrenal cortex	UBERON:0001235	84.68	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.74	gold quality
adrenal gland	UBERON:0002369	81.93	gold quality
hypothalamus	UBERON:0001898	81.55	gold quality
nucleus accumbens	UBERON:0001882	79.14	gold quality
prefrontal cortex	UBERON:0000451	78.69	gold quality
caudate nucleus	UBERON:0001873	78.08	gold quality
right frontal lobe	UBERON:0002810	77.19	gold quality
putamen	UBERON:0001874	76.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	76.95	gold quality
substantia nigra	UBERON:0002038	76.43	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	76.26	gold quality
anterior cingulate cortex	UBERON:0009835	76.13	gold quality
substantia nigra pars compacta	UBERON:0001965	75.67	gold quality
frontal cortex	UBERON:0001870	75.62	gold quality
cerebellar cortex	UBERON:0002129	75.44	gold quality
cerebellar hemisphere	UBERON:0002245	75.39	gold quality
cerebellum	UBERON:0002037	75.33	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.17	gold quality
neocortex	UBERON:0001950	75.15	gold quality
midbrain	UBERON:0001891	74.64	gold quality
tibia	UBERON:0000979	74.53	gold quality
lateral nuclear group of thalamus	UBERON:0002736	74.44	silver quality
substantia nigra pars reticulata	UBERON:0001966	74.41	silver quality
apex of heart	UBERON:0002098	73.83	gold quality
primary visual cortex	UBERON:0002436	73.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting FAM43B, 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-9-5P	100.00	72.28	2361
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-133A-3P	99.27	71.53	1270
HSA-MIR-133B	99.27	71.53	1270
HSA-MIR-642A-3P	99.23	67.67	1258
HSA-MIR-642B-3P	99.23	67.67	1258

Literature-anchored findings (GeneRIF, showing 1)

• expression of FAM43B, regulated by methylation and epigenetic silencing could contribute to hepatocellular carcinoma tumorigenesis by regulating cell proliferation (PMID:21461611)

Cross-species orthologs

13 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam43b	ENSDARG00000070222
mus_musculus	Fam43b	ENSMUSG00000078235
rattus_norvegicus	Fam43b	ENSRNOG00000078542
drosophila_melanogaster	Dab	FBGN0000414
drosophila_melanogaster	numb	FBGN0002973
drosophila_melanogaster	CG8312	FBGN0037720
drosophila_melanogaster	Aplip1	FBGN0040281
drosophila_melanogaster	CG42673	FBGN0261555
caenorhabditis_elegans		WBGENE00000894
caenorhabditis_elegans		WBGENE00001116
caenorhabditis_elegans		WBGENE00002176
caenorhabditis_elegans		WBGENE00003830
caenorhabditis_elegans		WBGENE00009930

Paralogs (11): MAPK8IP2 (ENSG00000008735), NUMBL (ENSG00000105245), MAPK8IP1 (ENSG00000121653), NUMB (ENSG00000133961), GULP1 (ENSG00000144366), DAB2 (ENSG00000153071), LDLRAP1 (ENSG00000157978), DAB1 (ENSG00000173406), FAM43A (ENSG00000185112), NOS1AP (ENSG00000198929), C1orf226 (ENSG00000239887)

Protein

Protein identifiers

Protein FAM43B — Q6ZT52 (reviewed: Q6ZT52)

All UniProt accessions (1): Q6ZT52

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM43 family.

RefSeq proteins (1): NP_997217* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006020	PTB/PI_dom	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR033930	FAM43A/B_PTB	Domain
IPR051133	Adapter_Engulfment-Domain	Family

Pfam: PF14719

UniProt features (5 total): compositionally biased region 2, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZT52-F1	69.91	0.33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 43 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, CREL_01, BENPORATH_ES_WITH_H3K27ME3, RIGGI_EWING_SARCOMA_PROGENITOR_UP, TGGAAA_NFAT_Q4_01, NFAT_Q6, chr1p36, MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MIKKELSEN_NPC_HCP_WITH_H3K27ME3, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, NFKAPPAB65_01, E2F3_UP.V1_UP, GSE10239_KLRG1INT_VS_KLRG1HIGH_EFF_CD8_TCELL_UP, MIR3158_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

422 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM43B	PRR18	Q8N4B5	495
FAM43B	CAMK2N1	Q7Z7J9	433
FAM43B	RSPH9	Q9H1X1	411
FAM43B	GOLGA7B	Q2TAP0	406
FAM43B	TMEM198	Q66K66	397
FAM43B	GLYATL2	Q8WU03	391
FAM43B	TENT5B	Q96A09	373
FAM43B	EVA1A	Q9H8M9	369
FAM43B	CPNE2	Q96FN4	366
FAM43B	FAM13C	Q8NE31	364
FAM43B	KCTD4	Q8WVF5	359
FAM43B	MUL1	Q969V5	351
FAM43B	FSTL4	Q6MZW2	349
FAM43B	CCDC182	A6NF36	329
FAM43B	TSPAN17	Q96FV3	317

IntAct

3 interactions, top by confidence:

A	B	Type	Score
PIPSL	C1orf226	psi-mi:“MI:0914”(association)	0.350
FTL		psi-mi:“MI:0914”(association)	0.350

BioGRID (2): FAM43B (Affinity Capture-RNA), FAM43B (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5KY20, A2A9Q0, A9JSM3, C9JI98, D4A2Q0, D4ABX8, E7ERA6, F1SAM7, F2Z333, O94819, P0C7J6, P0CG25, P13224, P56400, Q04785, Q0GA42, Q17QZ8, Q1RMK9, Q2MJR0, Q2WF71, Q504Y2, Q50LG9, Q5RJI4, Q6IEE6, Q6IEE7, Q6IQX7, Q6P6N5, Q6PJG9, Q6UKI2, Q6UX72, Q6ZMC9, Q6ZT52, Q6ZVX7, Q7Z6J2, Q80XU8, Q86UD0, Q86VR8, Q8BQB4, Q8IZ52, Q8QZV0

Diamond homologs: Q6ZT52, Q8BUP8, Q8N2R8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

14 predictions. Top by Δscore:

Variant	Effect	Δscore
1:20552895:G:GA	acceptor_gain	0.4500
1:20553811:G:GT	donor_gain	0.4300
1:20553867:G:GT	donor_gain	0.3700
1:20552893:C:A	acceptor_gain	0.3500
1:20553838:G:GT	donor_gain	0.3500
1:20552892:T:TA	acceptor_gain	0.3300
1:20553812:G:T	donor_gain	0.3000
1:20553261:C:T	donor_gain	0.2800
1:20552896:C:A	acceptor_gain	0.2700
1:20554395:AGAGG:A	acceptor_gain	0.2600
1:20553843:GCTC:G	donor_gain	0.2200
1:20554524:G:C	acceptor_gain	0.2200
1:20554393:GGAGA:G	acceptor_gain	0.2100
1:20554394:GAGAG:G	acceptor_gain	0.2100

AlphaMissense

2099 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:20553206:G:T	G78V	1.000
1:20553454:T:A	W161R	1.000
1:20553454:T:C	W161R	1.000
1:20553205:G:C	G78R	0.999
1:20553206:G:A	G78D	0.999
1:20553308:T:C	L112P	0.999
1:20553456:G:C	W161C	0.999
1:20553456:G:T	W161C	0.999
1:20553499:T:C	C176R	0.999
1:20553501:C:G	C176W	0.999
1:20553506:C:A	A178D	0.999
1:20553586:T:C	F205L	0.999
1:20553587:T:C	F205S	0.999
1:20553588:C:A	F205L	0.999
1:20553588:C:G	F205L	0.999
1:20553199:T:C	Y76H	0.998
1:20553199:T:G	Y76D	0.998
1:20553200:A:G	Y76C	0.998
1:20553205:G:T	G78C	0.998
1:20553394:T:G	Y141D	0.998
1:20553410:T:A	I146N	0.998
1:20553410:T:C	I146T	0.998
1:20553410:T:G	I146S	0.998
1:20553449:T:C	F159S	0.998
1:20553455:G:C	W161S	0.998
1:20553458:T:A	V162D	0.998
1:20553460:T:G	Y163D	0.998
1:20553463:C:A	R164S	0.998
1:20553500:G:A	C176Y	0.998
1:20553502:C:G	H177D	0.998

dbSNP variants (sampled 300 via entrez): RS1000088146 (1:20554363 C>T), RS1000512705 (1:20550909 G>C), RS1000569514 (1:20550615 T>G), RS1000635603 (1:20554802 T>C), RS1001861541 (1:20555221 G>A), RS1001933646 (1:20551722 G>C), RS1002546185 (1:20555401 A>C,G), RS1003861685 (1:20551776 G>C), RS1004011133 (1:20553348 G>A,T), RS1004492465 (1:20553373 G>A,C,T), RS1004550216 (1:20552083 C>A,T), RS1006387505 (1:20555113 G>A), RS1006487605 (1:20553522 G>A), RS1006617384 (1:20553186 C>T), RS1006729349 (1:20550880 T>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

6 associations (top):

Study	Trait	p-value
GCST005316_432	Intelligence (MTAG)	2.000000e-10
GCST005316_434	Intelligence (MTAG)	3.000000e-10
GCST006269_325	General cognitive ability	3.000000e-10
GCST006269_326	General cognitive ability	3.000000e-10
GCST012616_3	Spondylosis	9.000000e-07
GCST90011900_28	Serum alkaline phosphatase levels	3.000000e-17

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression	2
propionaldehyde	increases expression	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
entinostat	increases expression	1
nutlin 3	affects cotreatment, increases expression	1
Grape Seed Proanthocyanidins	decreases expression, affects cotreatment	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression	1
Temozolomide	decreases expression	1
Decitabine	affects expression	1
Sunitinib	decreases expression	1
Leflunomide	decreases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	increases methylation	1
Calcitriol	increases expression	1
Camptothecin	increases expression	1
Catechin	affects cotreatment, decreases expression	1
Cisplatin	affects expression	1
Dactinomycin	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Lead	affects expression	1
Niclosamide	increases expression	1
Rotenone	increases expression	1
Urethane	increases expression	1
Valproic Acid	affects expression	1
Antirheumatic Agents	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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