FAM43A

Summary

FAM43A (family with sequence similarity 43 member A, HGNC:26888) is a protein-coding gene on chromosome 3q29, encoding Protein FAM43A (Q8N2R8).

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 68 total
• MANE Select transcript: NM_153690

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26888
Approved symbol	FAM43A
Name	family with sequence similarity 43 member A
Location	3q29
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90022
Ensembl gene	ENSG00000185112
Ensembl biotype	protein_coding
Entrez	131583

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000329759

RefSeq mRNA: 1 — MANE Select: NM_153690 NM_153690

CCDS: CCDS33923

Canonical transcript exons

ENST00000329759 — 1 exons

Exon	Start	End
ENSE00001331401	194685883	194689037

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 93.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.0118 / max 551.3540, expressed in 1598 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
40669	27.6320	1595
40668	1.1398	313
40670	0.2399	118

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pons	UBERON:0000988	93.05	gold quality
tendon of biceps brachii	UBERON:0008188	91.76	gold quality
spleen	UBERON:0002106	91.50	gold quality
penis	UBERON:0000989	91.14	gold quality
gingival epithelium	UBERON:0001949	90.76	gold quality
stromal cell of endometrium	CL:0002255	90.35	gold quality
gingiva	UBERON:0001828	89.89	gold quality
lower lobe of lung	UBERON:0008949	88.56	gold quality
left ventricle myocardium	UBERON:0006566	88.43	gold quality
mammalian vulva	UBERON:0000997	88.36	gold quality
renal medulla	UBERON:0000362	87.79	gold quality
ileal mucosa	UBERON:0000331	87.68	gold quality
upper leg skin	UBERON:0004262	87.21	gold quality
kidney epithelium	UBERON:0004819	87.19	silver quality
apex of heart	UBERON:0002098	87.17	gold quality
placenta	UBERON:0001987	86.98	gold quality
granulocyte	CL:0000094	86.65	gold quality
heart right ventricle	UBERON:0002080	86.12	gold quality
skin of hip	UBERON:0001554	86.06	gold quality
metanephros cortex	UBERON:0010533	85.31	gold quality
omental fat pad	UBERON:0010414	85.23	gold quality
peritoneum	UBERON:0002358	85.15	gold quality
left uterine tube	UBERON:0001303	85.12	gold quality
skin of abdomen	UBERON:0001416	85.07	gold quality
skin of leg	UBERON:0001511	84.93	gold quality
adipose tissue of abdominal region	UBERON:0007808	84.92	gold quality
tibialis anterior	UBERON:0001385	84.32	silver quality
upper arm skin	UBERON:0004263	83.92	gold quality
esophagus squamous epithelium	UBERON:0006920	83.88	gold quality
zone of skin	UBERON:0000014	83.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-8205	yes	84.79
E-CURD-114	yes	10.60
E-ANND-3	yes	5.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

77 targeting FAM43A, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6867-5P	100.00	82.21	3464
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-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-130A-3P	99.90	73.31	1861

Cross-species orthologs

13 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam43a	ENSDARG00000043009
mus_musculus	Fam43a	ENSMUSG00000046546
rattus_norvegicus	Fam43a	ENSRNOG00000001728
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), FAM43B (ENSG00000183114), NOS1AP (ENSG00000198929), C1orf226 (ENSG00000239887)

Protein

Protein identifiers

Protein FAM43A — Q8N2R8 (reviewed: Q8N2R8)

All UniProt accessions (1): Q8N2R8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM43 family.

RefSeq proteins (1): NP_710157* (*=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 (10 total): compositionally biased region 4, region of interest 3, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N2R8-F1	63.85	0.22

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 185 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, GSE45365_NK_CELL_VS_BCELL_UP, PEREZ_TP63_TARGETS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, CORRE_MULTIPLE_MYELOMA_UP, LEI_HOXC8_TARGETS_DN, PEREZ_TP53_AND_TP63_TARGETS, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, BASAKI_YBX1_TARGETS_DN, CUI_TCF21_TARGETS_2_DN, RIGGI_EWING_SARCOMA_PROGENITOR_UP, TTTGCAC_MIR19A_MIR19B, BOYLAN_MULTIPLE_MYELOMA_C_D_UP, MARSON_BOUND_BY_FOXP3_STIMULATED

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

368 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM43A	LSG1	Q9H089	579
FAM43A	TMEM44	Q2T9K0	505
FAM43A	SFT2D1	Q8WV19	489
FAM43A	SNX29	Q8TEQ0	479
FAM43A	XXYLT1	Q8NBI6	460
FAM43A	ZNF22	P17026	441
FAM43A	NEURL1B	A8MQ27	406
FAM43A	SCLY	Q96I15	395
FAM43A	SLC66A2	Q8N2U9	382
FAM43A	PLEKHF2	Q9H8W4	379
FAM43A	STOX1	Q6ZVD7	368
FAM43A	PIP4P2	Q8N4L2	360
FAM43A	ARRDC3	Q96B67	357
FAM43A	PLEKHG1	Q9ULL1	357
FAM43A	PLEKHH2	Q8IVE3	356

IntAct

15 interactions, top by confidence:

A	B	Type	Score
CLASP2	YWHAZ	psi-mi:“MI:0914”(association)	0.670
GTF2H2C	FAM43A	psi-mi:“MI:0915”(physical association)	0.560
RBBP4	TNRC18	psi-mi:“MI:0914”(association)	0.530
FAM43A	FTL	psi-mi:“MI:0914”(association)	0.530
FAM43A	GRN	psi-mi:“MI:0914”(association)	0.530
CLASP2	FAM43A	psi-mi:“MI:0915”(physical association)	0.400
FAM43A	PPP2R1B	psi-mi:“MI:0914”(association)	0.350
PIPSL	C1orf226	psi-mi:“MI:0914”(association)	0.350
FAM43A	IFT56	psi-mi:“MI:0914”(association)	0.350
FTL	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
FTL		psi-mi:“MI:0914”(association)	0.350
SERPINA12	COQ9	psi-mi:“MI:0914”(association)	0.350
GTF2H2C	FAM43A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (52): FAM43A (Affinity Capture-MS), AKAP11 (Affinity Capture-MS), WRAP53 (Affinity Capture-MS), PPP2R1B (Affinity Capture-MS), PPP2R5C (Affinity Capture-MS), PPP2R5D (Affinity Capture-MS), PPP2R5A (Affinity Capture-MS), PPP2R5B (Affinity Capture-MS), PPP2R5E (Affinity Capture-MS), TBL3 (Affinity Capture-MS), CBWD1 (Affinity Capture-MS), SNX6 (Affinity Capture-MS), FAM43A (Biochemical Activity), PPP2R5E (Affinity Capture-MS), PPP2R5A (Affinity Capture-MS)

ESM2 similar proteins: A0A8I3NFE2, A0FI79, A1A5B6, A4D2P6, D7PF45, F1LXF1, O15357, O60346, O75808, P11274, P49796, P52734, P53349, P59672, P70268, P78524, P98174, Q0QWG9, Q13233, Q13905, Q16825, Q3MII6, Q50H33, Q5RDA9, Q62925, Q63433, Q6NS60, Q6P549, Q6PDJ6, Q6WVG3, Q7Z5H3, Q8BL80, Q8BUP8, Q8N2R8, Q8TF61, Q8VHK2, Q8WXD9, Q924W7, Q92625, Q96CX2

Diamond homologs: Q6ZT52, Q8BUP8, Q8N2R8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	64
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

27 predictions. Top by Δscore:

Variant	Effect	Δscore
3:194687749:T:G	donor_gain	0.4100
3:194687749:T:TG	donor_gain	0.3900
3:194687796:GCGC:G	donor_gain	0.3200
3:194687735:G:GA	donor_gain	0.3100
3:194687793:G:T	donor_gain	0.3100
3:194687877:GC:G	donor_gain	0.3100
3:194687723:GC:G	donor_gain	0.2900
3:194687734:T:TA	donor_gain	0.2900
3:194687792:G:GT	donor_gain	0.2600
3:194687737:T:TA	donor_gain	0.2500
3:194686551:ATTCT:A	donor_gain	0.2400
3:194687753:G:GG	donor_gain	0.2400
3:194687752:A:AG	donor_gain	0.2300
3:194686604:C:G	donor_gain	0.2200
3:194687158:TGACG:T	donor_loss	0.2200
3:194687159:GACGG:G	donor_loss	0.2200
3:194687160:ACG:A	donor_loss	0.2200
3:194687161:CG:C	donor_loss	0.2200
3:194687162:GGTG:G	donor_loss	0.2200
3:194687163:GTG:G	donor_loss	0.2200
3:194687164:T:TT	donor_loss	0.2200
3:194687165:GAG:G	donor_loss	0.2200
3:194687166:A:AT	donor_loss	0.2200
3:194687167:G:C	donor_loss	0.2200
3:194687720:GCAGC:G	donor_gain	0.2000
3:194687725:G:GG	donor_gain	0.2000
3:194687792:G:T	donor_gain	0.2000

AlphaMissense

2717 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:194687052:G:C	G76R	1.000
3:194687053:G:A	G76D	1.000
3:194687053:G:T	G76V	1.000
3:194687158:T:C	L111P	1.000
3:194687175:G:C	G117R	1.000
3:194687175:G:T	G117C	1.000
3:194687176:G:A	G117D	1.000
3:194687176:G:T	G117V	1.000
3:194687179:T:A	I118N	1.000
3:194687229:T:G	Y135D	1.000
3:194687245:T:A	V140D	1.000
3:194687287:C:A	A154D	1.000
3:194687289:T:A	W155R	1.000
3:194687289:T:C	W155R	1.000
3:194687291:G:C	W155C	1.000
3:194687291:G:T	W155C	1.000
3:194687301:C:G	H159D	1.000
3:194687334:T:C	C170R	1.000
3:194687336:C:G	C170W	1.000
3:194687337:C:G	H171D	1.000
3:194687339:C:A	H171Q	1.000
3:194687339:C:G	H171Q	1.000
3:194687341:C:A	A172D	1.000
3:194687421:T:C	F199L	1.000
3:194687422:T:C	F199S	1.000
3:194687422:T:G	F199C	1.000
3:194687423:T:A	F199L	1.000
3:194687423:T:G	F199L	1.000
3:194687014:T:A	I63N	0.999
3:194687041:T:A	V72E	0.999

dbSNP variants (sampled 300 via entrez): RS1000240679 (3:194689241 G>A), RS1000294655 (3:194689486 C>A,T), RS1001131485 (3:194685429 T>C), RS1001476265 (3:194685160 A>G), RS1002032660 (3:194684334 T>A,C), RS1002687759 (3:194687208 C>T), RS1002762068 (3:194685995 A>G), RS1003450257 (3:194688952 A>G), RS1003478320 (3:194689208 G>A), RS1004011761 (3:194688898 G>A), RS1004047025 (3:194686765 G>A,C,T), RS1004147481 (3:194688653 A>G,T), RS1006605761 (3:194684857 C>A,T), RS1006713750 (3:194689203 G>A,T), RS1006767831 (3:194689473 C>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

7 associations (top):

Study	Trait	p-value
GCST004600_197	Eosinophil percentage of white cells	3.000000e-10
GCST004617_92	Eosinophil percentage of granulocytes	1.000000e-10
GCST004623_32	Neutrophil percentage of granulocytes	2.000000e-09
GCST90002381_199	Eosinophil count	3.000000e-10
GCST90002382_588	Eosinophil percentage of white cells	3.000000e-14
GCST90002398_439	Neutrophil count	1.000000e-11
GCST90002399_410	Neutrophil percentage of white cells	3.000000e-11

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0007991	eosinophil percentage of leukocytes
EFO:0007996	eosinophil percentage of granulocytes
EFO:0007994	neutrophil percentage of granulocytes
EFO:0004842	eosinophil count
EFO:0004833	neutrophil count
EFO:0007990	neutrophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, affects cotreatment	6
Benzo(a)pyrene	increases expression, increases methylation	5
trichostatin A	affects cotreatment, increases expression	3
Arsenic	decreases expression, increases abundance, affects methylation, increases expression	3
Estradiol	decreases expression, increases expression	3
Cyclosporine	affects expression, increases expression	3
sodium arsenite	increases expression	2
entinostat	increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tetrachlorodibenzodioxin	affects reaction, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	2
Particulate Matter	decreases expression, increases abundance	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
propionaldehyde	increases expression	1
bisphenol A	increases expression	1
sodium arsenate	decreases expression, increases abundance	1
2-methyl-4-isothiazolin-3-one	increases expression	1
quercitrin	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	decreases expression	1
arsenite	increases methylation	1
afimoxifene	decreases reaction, decreases expression	1
sulforaphane	increases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	increases expression	1
zinc chromate	increases abundance, increases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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