FAM240A

Summary

FAM240A (family with sequence similarity 240 member A, HGNC:52390) is a protein-coding gene on chromosome 3p21.31, encoding Protein FAM240A (A0A1B0GVK7).

At a glance

• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001195442

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:52390
Approved symbol	FAM240A
Name	family with sequence similarity 240 member A
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283473
Ensembl biotype	protein_coding
Entrez	100132146

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000640551

RefSeq mRNA: 1 — MANE Select: NM_001195442 NM_001195442

CCDS: CCDS82764

Canonical transcript exons

ENST00000640551 — 3 exons

Exon	Start	End
ENSE00001673107	46617183	46617328
ENSE00001696450	46625128	46626543
ENSE00003893505	46612525	46612698

Expression profiles

Bgee: expression breadth broad, 37 present calls, max score 76.60.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.60	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	58.51	gold quality
hindlimb stylopod muscle	UBERON:0004252	48.80	gold quality
adult mammalian kidney	UBERON:0000082	47.04	gold quality
saliva-secreting gland	UBERON:0001044	45.60	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	45.11	gold quality
skeletal muscle tissue	UBERON:0001134	44.74	silver quality
minor salivary gland	UBERON:0001830	44.28	gold quality
heart left ventricle	UBERON:0002084	44.09	gold quality
apex of heart	UBERON:0002098	43.93	silver quality
kidney	UBERON:0002113	42.88	gold quality
lower esophagus mucosa	UBERON:0035834	42.27	silver quality
right atrium auricular region	UBERON:0006631	41.76	gold quality
heart	UBERON:0000948	41.20	gold quality
right lobe of liver	UBERON:0001114	39.99	silver quality
muscle tissue	UBERON:0002385	39.41	silver quality
calcaneal tendon	UBERON:0003701	38.97	gold quality
metanephros cortex	UBERON:0010533	38.79	silver quality
muscle of leg	UBERON:0001383	38.38	gold quality
gastrocnemius	UBERON:0001388	37.49	gold quality
adrenal tissue	UBERON:0018303	37.25	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
left lobe of thyroid gland	UBERON:0001120	36.69	silver quality
right lobe of thyroid gland	UBERON:0001119	36.50	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
sural nerve	UBERON:0015488	36.28	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
Ammon’s horn	UBERON:0001954	36.01	silver quality
granulocyte	CL:0000094	35.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting FAM240A, 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-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-4804-3P	99.65	67.78	866
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-199A-5P	99.51	69.71	1107
HSA-MIR-199B-5P	99.51	69.74	1098
HSA-MIR-4325	99.49	72.20	1342
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-147B-5P	99.45	70.62	2432

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam240a	ENSMUSG00000096393

Paralogs (1): FAM240B (ENSG00000283329)

Protein

Protein identifiers

Protein FAM240A — A0A1B0GVK7 (reviewed: A0A1B0GVK7)

All UniProt accessions (1): A0A1B0GVK7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM240 family.

RefSeq proteins (1): NP_001182371* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040261	FAM240	Family

UniProt features (2 total): chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GVK7-F1	80.64	0.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 11 (showing top): chr3p21, MIR4492, MIR92A_2_5P, MIR876_5P, MIR3167, MIR6817_5P, MIR4769_3P, MIR7703, MIR592, MIR509_3P, MIR3650

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

132 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM240A	CCDC78	A2IDD5	509
FAM240A	DNALI1	O14645	432
FAM240A	TRIM58	Q8NG06	431
FAM240A	SCGB3A1	Q96QR1	370
FAM240A	FOXJ1	Q92949	279
FAM240A	PRSS22	Q9GZN4	277
FAM240A	GFRA1	P56159	248
FAM240A	SIGLEC10	Q96LC7	165
FAM240A	LRRC2	Q9BYS8	162
FAM240A	GRAP2	O75791	159
FAM240A	RTP3	Q9BQQ7	153
FAM240A	LRRC39	Q96DD0	115
FAM240A	S100A8	P05109	95
FAM240A	PLIN1	O60240	89
FAM240A	ARID4B	Q4LE39	86
FAM240A	ARID4A	P29374	86

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GVK7, A6ZT44, A7RHB3, C0H3T6, G2TRJ6, G3UWD5, H3BU77, J3QM76, O14183, O29949, O74506, O97980, P0CT00, P0CT01, P0DXN9, P15960, P22384, P25575, P27975, P27982, P36340, P38839, P42172, P50628, P68353, P80594, P92538, P93301, Q00147, Q10486, Q14236, Q16048, Q1X6Y7, Q1X6Z0, Q32P96, Q3E795, Q3E7K4, Q3V4X0, Q495D7, Q5K130

Diamond homologs: A0A1B0GVK7, A0A1B0GVZ2, A0A1B0GVR7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

538 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000048952 (3:46625649 T>C,G), RS1000197136 (3:46619259 G>A), RS1000205586 (3:46615630 T>C,G), RS1000591338 (3:46624217 A>G), RS1000649650 (3:46626986 T>C), RS1000661886 (3:46620709 G>C), RS1000695739 (3:46623915 T>A,C), RS1000724212 (3:46615848 A>G), RS1001204645 (3:46619112 C>T), RS1001211508 (3:46613366 C>A,T), RS1001306169 (3:46618737 G>T), RS1001326268 (3:46617245 G>A), RS1001387063 (3:46611677 G>A), RS1001537552 (3:46625036 T>C), RS1001652431 (3:46622067 T>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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