FAM47E

Summary

FAM47E (family with sequence similarity 47 member E, HGNC:34343) is a protein-coding gene on chromosome 4q21.1, encoding Protein FAM47E (Q6ZV65). Promotes histone methylation by localizing the arginine methyltransferase PRMT5 to chromatin.

Enables enzyme activator activity. Involved in protein localization to chromatin and transcription initiation-coupled chromatin remodeling. Located in chromatin; cytoplasm; and nucleus.

Source: NCBI Gene 100129583 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 55 total
• MANE Select transcript: NM_001136570

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34343
Approved symbol	FAM47E
Name	family with sequence similarity 47 member E
Location	4q21.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ42946, LOC100129583
Ensembl gene	ENSG00000189157
Ensembl biotype	protein_coding
Entrez	100129583

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 11 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000424749, ENST00000502320, ENST00000510197, ENST00000510328, ENST00000511946, ENST00000512895, ENST00000515589, ENST00000606246, ENST00000606550, ENST00000853410, ENST00000853411, ENST00000946090, ENST00000946091, ENST00000946092

RefSeq mRNA: 2 — MANE Select: NM_001136570 NM_001136570, NM_001242936

CCDS: CCDS47081, CCDS58907

Canonical transcript exons

ENST00000424749 — 8 exons

Exon	Start	End
ENSE00001368455	76280264	76280341
ENSE00002058265	76283381	76283783
ENSE00002063678	76251721	76251820
ENSE00003696777	76271568	76271768
ENSE00003696825	76256178	76256523
ENSE00003697204	76278069	76278224
ENSE00003699808	76268660	76268768
ENSE00003700173	76263704	76263843

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 91.90.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1658 / max 69.0127, expressed in 43 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
48324	2.7740	589
48326	0.1015	31
48325	0.0643	22
48322	0.0501	18
48323	0.0310	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	91.90	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.36	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.65	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.98	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.10	gold quality
anterior cingulate cortex	UBERON:0009835	84.52	gold quality
islet of Langerhans	UBERON:0000006	84.20	gold quality
hypothalamus	UBERON:0001898	83.90	gold quality
adenohypophysis	UBERON:0002196	83.51	gold quality
right frontal lobe	UBERON:0002810	83.39	gold quality
prefrontal cortex	UBERON:0000451	83.22	gold quality
body of pancreas	UBERON:0001150	83.00	gold quality
spinal cord	UBERON:0002240	81.88	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.79	gold quality
pancreas	UBERON:0001264	81.57	gold quality
left lobe of thyroid gland	UBERON:0001120	81.12	gold quality
amygdala	UBERON:0001876	81.05	gold quality
hindlimb stylopod muscle	UBERON:0004252	80.71	gold quality
thyroid gland	UBERON:0002046	79.81	gold quality
pituitary gland	UBERON:0000007	79.78	gold quality
right lobe of thyroid gland	UBERON:0001119	79.25	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	79.03	gold quality
right testis	UBERON:0004534	78.78	gold quality
metanephros cortex	UBERON:0010533	78.54	gold quality
nucleus accumbens	UBERON:0001882	78.35	gold quality
left testis	UBERON:0004533	77.66	gold quality
mucosa of transverse colon	UBERON:0004991	76.59	gold quality
neocortex	UBERON:0001950	76.27	gold quality
caudate nucleus	UBERON:0001873	75.96	gold quality
muscle of leg	UBERON:0001383	75.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting FAM47E, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
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-3064-3P	100.00	70.09	1254
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-409-3P	99.50	66.33	1192
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-4480	99.42	66.02	735
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-1253	99.12	67.08	1688
HSA-MIR-548L	99.06	70.90	2560
HSA-MIR-4699-5P	98.99	67.50	1210
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-4662A-5P	98.48	67.18	1007
HSA-MIR-532-5P	98.43	67.53	760
HSA-MIR-1262	98.17	66.52	757
HSA-MIR-4701-3P	98.17	66.25	788
HSA-MIR-6736-5P	98.17	66.43	760
HSA-MIR-3144-3P	98.15	67.34	677
HSA-MIR-744-3P	97.99	67.76	637

Literature-anchored findings (GeneRIF, showing 2)

• Findings suggested that STX1B rs4889603, FAM47E rs6812193 and SCARB2 rs6825004 do not confer a significant risk for Parkinson’s disease (PMID:26224037)
• The uncharacterized protein FAM47E interacts with PRMT5 and regulates its functions. (PMID:33376131)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:158260	ENSDARG00000101703
mus_musculus	Fam47e	ENSMUSG00000057068
rattus_norvegicus	Fam47e	ENSRNOG00000062922
drosophila_melanogaster	Nf-YB	FBGN0032816
drosophila_melanogaster	tau	FBGN0266579
caenorhabditis_elegans		WBGENE00021132

Paralogs (2): DR1 (ENSG00000117505), NFYB (ENSG00000120837)

Protein

Protein identifiers

Protein FAM47E — Q6ZV65 (reviewed: Q6ZV65)

All UniProt accessions (5): A0A1B0GTQ8, A0A1B0GUL4, D6RBT2, Q6ZV65, U3KQR7

UniProt curated annotations — full annotation on UniProt →

Function. Promotes histone methylation by localizing the arginine methyltransferase PRMT5 to chromatin.

Subunit / interactions. Interacts with PRMT5; the interaction is direct. Interacts with WDR77.

Subcellular location. Nucleus. Chromosome. Cytoplasm.

Similarity. Belongs to the FAM47 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6ZV65-3	1	yes
Q6ZV65-2	2
Q6ZV65-1	3

RefSeq proteins (2): NP_001130042, NP_001229865 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032743	FAM47	Family

Pfam: PF14642

UniProt features (8 total): splice variant 4, sequence conflict 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZV65-F1	62.24	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): GOBP_PROTEIN_LOCALIZATION_TO_CHROMATIN, GOBP_PROTEIN_LOCALIZATION_TO_CHROMOSOME, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_TRANSCRIPTION_INITIATION_AT_RNA_POLYMERASE_II_PROMOTER, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_CHROMATIN_REMODELING, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, chr4q21, GOMF_ENZYME_ACTIVATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, GSE14415_FOXP3_KO_NATURAL_TREG_VS_TCONV_DN, ATF5_TARGET_GENES, BARX1_TARGET_GENES, CBX7_TARGET_GENES, CREB3L4_TARGET_GENES

GO Biological Process (3): transcription initiation-coupled chromatin remodeling (GO:0045815), protein localization to chromatin (GO:0071168), chromatin organization (GO:0006325)

GO Molecular Function (2): enzyme activator activity (GO:0008047), protein binding (GO:0005515)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), cytoplasm (GO:0005737), chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
transcription initiation at RNA polymerase II promoter	1
positive regulation of gene expression, epigenetic	1
protein localization to chromosome	1
cellular component organization	1
catalytic activity	1
enzyme regulator activity	1
molecular function activator activity	1
binding	1
chromosome	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

214 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM47E	CCDC62	Q6P9F0	580
FAM47E	LRRC74B	Q6ZQY2	530
FAM47E	MCCC1	Q96RQ3	480
FAM47E	OR2B2	Q9GZK3	449
FAM47E	NUCKS1	Q9H1E3	445
FAM47E	ACSM2A	Q08AH3	443
FAM47E	TMEM175	Q9BSA9	431
FAM47E	PLXDC1	Q8IUK5	417
FAM47E	CCDC158	Q5M9N0	407
FAM47E	SYT12	Q8IV01	397
FAM47E	ACMSD	Q8TDX5	394
FAM47E	SYT11	Q9BT88	375
FAM47E	STX1B	P61266	370
FAM47E	STBD1	O95210	370
FAM47E	LMNTD1	Q8N9Z9	370

IntAct

7 interactions, top by confidence:

A	B	Type	Score
FAM47E	PRMT5	psi-mi:“MI:0915”(physical association)	0.400
FAM47E		psi-mi:“MI:0915”(physical association)	0.400
FAM47E	DCLK1	psi-mi:“MI:0915”(physical association)	0.400
FAM47E	PTX3	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (14): FAM47E-STBD1 (Two-hybrid), FAM47E-STBD1 (Two-hybrid), FAM47E-STBD1 (Negative Genetic), FAM47E (Two-hybrid), FAM47E (Affinity Capture-Western), PRMT5 (Affinity Capture-Western), WDR77 (Affinity Capture-Western), PRMT5 (Reconstituted Complex), FAM47E-STBD1 (Proximity Label-MS), FAM47E-STBD1 (Proximity Label-MS), FAM47E (Cross-Linking-MS (XL-MS)), FAM47E (Affinity Capture-MS), FAM47E (Affinity Capture-MS), FAM47E-STBD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVB3, A0A1B0GVH6, A2RRY8, A4IGV6, A6NHR8, B3DHS1, E1B9I5, O74317, O95561, P03319, P03320, P0C9Z5, P0C9Z6, P10260, P36353, P40744, P40745, Q06616, Q09280, Q09424, Q2KIL1, Q2KIR0, Q32KT7, Q32LB6, Q3T028, Q3TTI8, Q496A3, Q5NC83, Q5SQS8, Q5XIU7, Q68FQ8, Q6DFB0, Q6ZNM6, Q6ZV65, Q811V6, Q8IWA6, Q8N9R6, Q8R0E5, Q8TAL5, Q8WTQ4

Diamond homologs: A6NHR8, Q5JRC9, Q6ZV65, Q8NA70, Q5HY64

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1602 predictions. Top by Δscore:

Variant	Effect	Δscore
4:76263702:A:AG	acceptor_gain	1.0000
4:76263703:G:GG	acceptor_gain	1.0000
4:76263839:GGACC:G	donor_gain	1.0000
4:76263840:GACCG:G	donor_gain	1.0000
4:76263844:G:GG	donor_gain	1.0000
4:76268658:A:AG	acceptor_gain	1.0000
4:76268659:G:GG	acceptor_gain	1.0000
4:76268778:GCA:G	donor_gain	1.0000
4:76268781:G:GG	donor_gain	1.0000
4:76268798:G:GG	donor_gain	1.0000
4:76268814:G:GG	donor_gain	1.0000
4:76251816:TCCAG:T	donor_loss	0.9900
4:76251817:CCAG:C	donor_loss	0.9900
4:76251819:AGG:A	donor_loss	0.9900
4:76251820:GGT:G	donor_loss	0.9900
4:76251821:G:GC	donor_loss	0.9900
4:76251821:GT:G	donor_loss	0.9900
4:76251822:T:A	donor_loss	0.9900
4:76263703:GCT:G	acceptor_gain	0.9900
4:76263703:GCTC:G	acceptor_gain	0.9900
4:76263782:A:T	donor_gain	0.9900
4:76263840:GACC:G	donor_gain	0.9900
4:76263841:ACC:A	donor_gain	0.9900
4:76268769:G:GG	donor_gain	0.9900
4:76268809:CTTTT:C	donor_gain	0.9900
4:76268810:TTTT:T	donor_gain	0.9900
4:76268818:G:GG	donor_gain	0.9900
4:76271764:CACAG:C	donor_loss	0.9900
4:76271765:ACAGG:A	donor_loss	0.9900
4:76271766:CAGG:C	donor_loss	0.9900

AlphaMissense

2577 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:76280309:T:C	F358L	0.967
4:76280311:C:A	F358L	0.967
4:76280311:C:G	F358L	0.967
4:76271607:T:C	F237L	0.944
4:76271609:T:A	F237L	0.944
4:76271609:T:G	F237L	0.944
4:76278132:T:A	W312R	0.933
4:76278132:T:C	W312R	0.933
4:76283381:T:C	F369L	0.927
4:76283383:C:A	F369L	0.927
4:76283383:C:G	F369L	0.927
4:76280300:T:C	F355L	0.924
4:76280302:T:A	F355L	0.924
4:76280302:T:G	F355L	0.924
4:76278134:G:C	W312C	0.912
4:76278134:G:T	W312C	0.912
4:76278111:T:A	W305R	0.898
4:76278111:T:C	W305R	0.898
4:76271592:T:C	F232L	0.889
4:76271594:C:A	F232L	0.889
4:76271594:C:G	F232L	0.889
4:76280310:T:C	F358S	0.880
4:76280301:T:C	F355S	0.875
4:76278095:G:C	K299N	0.855
4:76278095:G:T	K299N	0.855
4:76278113:G:C	W305C	0.843
4:76278113:G:T	W305C	0.843
4:76278133:G:C	W312S	0.835
4:76256443:T:C	F114L	0.833
4:76256445:C:A	F114L	0.833

dbSNP variants (sampled 300 via entrez): RS1000009445 (4:76270646 AG>A), RS1000019861 (4:76243081 T>C), RS1000102799 (4:76253011 G>A), RS1000121654 (4:76220875 C>T), RS1000125446 (4:76264298 A>G), RS1000182421 (4:76282296 T>C), RS1000346317 (4:76255497 C>T), RS1000377773 (4:76214037 C>T), RS1000379314 (4:76280048 G>A,T), RS1000434006 (4:76262440 T>A), RS10004443 (4:76226360 A>C,G,T), RS1000593195 (4:76247893 A>G,T), RS1000613728 (4:76269198 A>T), RS1000618167 (4:76282136 GA>G), RS1000660084 (4:76275983 G>A)

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

9 associations (top):

Study	Trait	p-value
GCST002544_18	Parkinson’s disease	3.000000e-11
GCST003984_10	Parkinson’s disease	7.000000e-11
GCST004902_47	Parkinson’s disease	1.000000e-14
GCST009325_78	Parkinson’s disease or first degree relation to individual with Parkinson’s disease	5.000000e-19
GCST009368_79	HDL cholesterol levels x long total sleep time interaction (2df test)	1.000000e-08
GCST012215_1	Alzheimer’s disease	5.000000e-09
GCST90002390_213	Mean corpuscular hemoglobin	2.000000e-10
GCST90011900_96	Serum alkaline phosphatase levels	2.000000e-12
GCST90013406_43	Liver enzyme levels (alkaline phosphatase)	8.000000e-16

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004527	mean corpuscular hemoglobin
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

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Smoke	increases abundance, increases expression, decreases expression	3
Air Pollutants	increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
bisphenol A	increases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
1-hydroxypyrene	affects cotreatment, decreases methylation	1
picene	decreases expression	1
Sunitinib	decreases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Cadmium	increases abundance, increases expression	1
Coal	increases abundance, increases expression	1
Estradiol	decreases expression	1
Methapyrilene	decreases methylation	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases methylation	1
Metals, Heavy	affects cotreatment, decreases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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