FAM47B

Summary

FAM47B (family with sequence similarity 47 member B, HGNC:26659) is a protein-coding gene on chromosome Xp21.1, encoding Protein FAM47B (Q8NA70).

At a glance

• Clinical variants (ClinVar): 113 total
• MANE Select transcript: NM_152631

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26659
Approved symbol	FAM47B
Name	family with sequence similarity 47 member B
Location	Xp21.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35782
Ensembl gene	ENSG00000189132
Ensembl biotype	protein_coding
Entrez	170062

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000329357

RefSeq mRNA: 1 — MANE Select: NM_152631 NM_152631

CCDS: CCDS14236

Canonical transcript exons

ENST00000329357 — 1 exons

Exon	Start	End
ENSE00001420065	34942796	34944915

Expression profiles

Bgee: expression breadth broad, 12 present calls, max score 86.30.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0539 / max 14.8858, expressed in 13 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
195879	0.0392	10
195878	0.0147	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	86.30	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.04	silver quality
left testis	UBERON:0004533	72.02	gold quality
right testis	UBERON:0004534	71.72	gold quality
testis	UBERON:0000473	70.82	gold quality
pancreatic ductal cell	CL:0002079	57.75	silver quality
adult organism	UBERON:0007023	55.85	gold quality
epithelial cell of pancreas	CL:0000083	54.38	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
tibialis anterior	UBERON:0001385	51.86	silver quality
myocardium	UBERON:0002349	50.25	gold quality
skin of hip	UBERON:0001554	49.65	silver quality
ileal mucosa	UBERON:0000331	48.38	silver quality
lower lobe of lung	UBERON:0008949	47.85	silver quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
quadriceps femoris	UBERON:0001377	46.53	gold quality
vastus lateralis	UBERON:0001379	45.40	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
upper leg skin	UBERON:0004262	42.81	silver quality
secondary oocyte	CL:0000655	42.57	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
cartilage tissue	UBERON:0002418	40.77	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting FAM47B, 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-4262	100.00	73.26	3931
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-545-5P	99.66	70.18	2308
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-3613-5P	98.40	68.91	604
HSA-MIR-6792-5P	98.39	68.16	1330
HSA-MIR-744-3P	97.99	67.76	637
HSA-MIR-3920	97.75	69.02	1168
HSA-MIR-6501-5P	97.41	68.24	712
HSA-MIR-4423-5P	95.24	64.42	454
HSA-MIR-5681B	94.82	69.30	514
HSA-MIR-503-3P	92.89	66.09	537

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	fmn2b	ENSDARG00000061778
danio_rerio	fhdc2	ENSDARG00000099767
drosophila_melanogaster	capu	FBGN0000256
drosophila_melanogaster	dia	FBGN0011202
drosophila_melanogaster	form3	FBGN0053556
drosophila_melanogaster	Frl	FBGN0267795
caenorhabditis_elegans		WBGENE00000872
caenorhabditis_elegans	fhod-1	WBGENE00016735
caenorhabditis_elegans		WBGENE00018976
caenorhabditis_elegans		WBGENE00019030
caenorhabditis_elegans	sydn-1	WBGENE00021473
caenorhabditis_elegans		WBGENE00021698

Paralogs (18): DAAM1 (ENSG00000100592), FNBP4 (ENSG00000109920), DIAPH1 (ENSG00000131504), FHOD3 (ENSG00000134775), FHOD1 (ENSG00000135723), FHDC1 (ENSG00000137460), DIAPH3 (ENSG00000139734), DAAM2 (ENSG00000146122), DIAPH2 (ENSG00000147202), FMN2 (ENSG00000155816), FMNL2 (ENSG00000157827), FMNL3 (ENSG00000161791), FMNL1 (ENSG00000184922), FAM47A (ENSG00000185448), SHTN1 (ENSG00000187164), FAM47C (ENSG00000198173), INF2 (ENSG00000203485), GRID2IP (ENSG00000215045)

Protein

Protein identifiers

Protein FAM47B — Q8NA70 (reviewed: Q8NA70)

All UniProt accessions (1): Q8NA70

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM47 family.

RefSeq proteins (1): NP_689844* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032743	FAM47	Family

Pfam: PF14642

UniProt features (9 total): compositionally biased region 3, sequence conflict 3, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NA70-F1	50.34	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, chrXp21, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, ZIM3_TARGET_GENES, ZNF22_TARGET_GENES, MIR3617_5P, MIR641, MIR6792_5P, MIR6501_5P, MIR744_3P, GSE17974_CTRL_VS_ACT_IL4_AND_ANTI_IL12_0.5H_CD4_TCELL_UP, GSE2706_R848_VS_LPS_2H_STIM_DC_UP, GSE6566_STRONG_VS_WEAK_DC_STIMULATED_CD4_TCELL_UP, GSE1112_OT1_CD8AB_VS_HY_CD8AA_THYMOCYTE_RTOC_CULTURE_DN, GSE1791_CTRL_VS_NEUROMEDINU_IN_T_CELL_LINE_6H_UP

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

446 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM47B	SATL1	Q86VE3	594
FAM47B	TMEM47	Q9BQJ4	581
FAM47B	TMEM191B	P0C7N4	576
FAM47B	MAP7D3	Q8IWC1	524
FAM47B	CFAP47	Q6ZTR5	524
FAM47B	OR13C8	Q8NGS7	507
FAM47B	ARSF	P54793	506
FAM47B	MAP3K15	Q6ZN16	480
FAM47B	MAGEB16	A2A368	448
FAM47B	LRRC14B	A6NHZ5	447
FAM47B	TMEM236	Q5W0B7	444
FAM47B	IL1RAPL1	Q9NZN1	441
FAM47B	LANCL3	Q6ZV70	437
FAM47B	TTC9	Q92623	412
FAM47B	ZCCHC13	Q8WW36	411

IntAct

8 interactions, top by confidence:

A	B	Type	Score
FAM47B	CARD10	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	FAM47B	psi-mi:“MI:0915”(physical association)	0.560
FAM47B	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
FAM47B	CARD10	psi-mi:“MI:0915”(physical association)	0.000
FAM47B	CCDC125	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): FAM47B (Reconstituted Complex), FAM47B (Two-hybrid), FAM47B (Two-hybrid), HIST1H2BN (Cross-Linking-MS (XL-MS)), HIST1H2BH (Cross-Linking-MS (XL-MS)), FAM47B (Cross-Linking-MS (XL-MS)), FAM47B (Cross-Linking-MS (XL-MS)), FAM47B (Cross-Linking-MS (XL-MS)), FAM47B (Cross-Linking-MS (XL-MS)), FAM47B (Cross-Linking-MS (XL-MS)), FAM47B (Cross-Linking-MS (XL-MS)), MIPEP (Cross-Linking-MS (XL-MS)), APP (Reconstituted Complex)

ESM2 similar proteins: A0A0B4J1W7, A0A1B0GUC4, A0JPK3, A4GZ95, A6NHN6, A6NJ64, A8MTZ7, E9PJ23, E9PJI5, E9PKD4, E9PQR5, F8W1W9, F8WFD2, O70889, O75200, O91083, O96001, P04605, P04614, P05909, P05910, P05911, P0C1J9, P0C1K3, P0C1K4, P0CK37, P0CK38, P0DM63, P0DXC3, P11263, P12453, P12513, P17759, P18098, P19507, P38900, Q02838, Q1A264, Q1HVG4, Q2YDJ5

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	25
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

41 predictions. Top by Δscore:

Variant	Effect	Δscore
X:34943857:CAG:C	acceptor_gain	0.9200
X:34943855:TCCAG:T	acceptor_gain	0.9100
X:34943856:CCAG:C	acceptor_gain	0.9100
X:34943858:A:AT	acceptor_gain	0.9100
X:34943859:G:T	acceptor_gain	0.9100
X:34943779:GTCC:G	donor_gain	0.7500
X:34943854:GTCCA:G	acceptor_gain	0.6900
X:34943189:G:GT	donor_gain	0.6500
X:34943778:TGTC:T	donor_gain	0.5800
X:34943848:TCGGG:T	acceptor_gain	0.5600
X:34943374:A:G	donor_gain	0.5400
X:34943414:C:CA	acceptor_gain	0.5400
X:34943635:GTCC:G	donor_gain	0.4500
X:34943738:G:GT	donor_gain	0.4400
X:34943358:C:G	donor_gain	0.4100
X:34943780:TCCA:T	donor_gain	0.4000
X:34943849:CGGGT:C	acceptor_gain	0.3600
X:34943850:GGGTG:G	acceptor_gain	0.3600
X:34943415:C:A	acceptor_gain	0.3500
X:34943781:C:G	donor_gain	0.3200
X:34943368:T:A	donor_gain	0.3000
X:34943594:G:GT	donor_gain	0.2800
X:34943865:TAC:T	acceptor_gain	0.2800
X:34943438:C:G	acceptor_gain	0.2700
X:34943847:ATCGG:A	acceptor_gain	0.2700
X:34943864:CTACT:C	acceptor_gain	0.2600
X:34944608:A:AC	acceptor_gain	0.2400
X:34943365:GTCTG:G	donor_gain	0.2300
X:34943357:C:A	donor_gain	0.2200
X:34943407:C:CT	acceptor_gain	0.2200

AlphaMissense

4208 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:34944614:T:C	F595L	0.983
X:34944616:C:A	F595L	0.983
X:34944616:C:G	F595L	0.983
X:34944610:G:C	K593N	0.982
X:34944610:G:T	K593N	0.982
X:34944605:T:C	F592L	0.977
X:34944607:T:A	F592L	0.977
X:34944607:T:G	F592L	0.977
X:34944662:T:C	F611L	0.976
X:34944664:T:A	F611L	0.976
X:34944664:T:G	F611L	0.976
X:34944606:T:C	F592S	0.968
X:34944639:T:C	M603T	0.954
X:34944663:T:C	F611S	0.954
X:34944235:G:C	W468C	0.953
X:34944235:G:T	W468C	0.953
X:34944615:T:C	F595S	0.952
X:34944618:T:A	I596N	0.952
X:34944227:T:C	F466L	0.951
X:34944229:C:A	F466L	0.951
X:34944229:C:G	F466L	0.951
X:34942979:T:C	F50L	0.949
X:34942981:T:A	F50L	0.949
X:34942981:T:G	F50L	0.949
X:34944693:T:A	V621D	0.945
X:34944233:T:A	W468R	0.940
X:34944233:T:C	W468R	0.940
X:34944621:T:C	L597P	0.938
X:34944611:G:C	D594H	0.936
X:34944618:T:C	I596T	0.933

dbSNP variants (sampled 300 via entrez): RS1001444390 (X:34942036 A>G), RS1001474972 (X:34941304 T>C,G), RS1002557863 (X:34942990 G>A,T), RS1003154042 (X:34943415 C>G,T), RS1004735324 (X:34941197 A>G,T), RS1005840715 (X:34945260 T>TG), RS1006435222 (X:34942932 A>G), RS1011375200 (X:34941503 G>A), RS10126846 (X:34944478 A>T), RS1016675300 (X:34944865 T>C), RS1016858007 (X:34945288 G>A), RS1019070279 (X:34942214 C>A,T), RS1021316758 (X:34944059 C>A,G,T), RS1022381905 (X:34941505 G>A), RS1022774109 (X:34942137 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
clothianidin	increases expression	1
Benzo(a)pyrene	affects methylation	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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