FAM50B

Summary

FAM50B (family with sequence similarity 50 member B, HGNC:18789) is a protein-coding gene on chromosome 6p25.2, encoding Protein FAM50B (Q9Y247).

This gene contains an intronless ORF that arose from ancestral retroposition. The encoded protein is related to a plant protein that plays a role in the circadian clock. This gene is adjacent to a differentially methylated region (DMR) and is imprinted and paternally expressed in many tissues.

Source: NCBI Gene 26240 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_012135

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18789
Approved symbol	FAM50B
Name	family with sequence similarity 50 member B
Location	6p25.2
Locus type	gene with protein product
Status	Approved
Aliases	D6S2654E, X5L
Ensembl gene	ENSG00000145945
Ensembl biotype	protein_coding
OMIM	614686
Entrez	26240

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000380274, ENST00000648326, ENST00000895441, ENST00000956903

RefSeq mRNA: 1 — MANE Select: NM_012135 NM_012135

CCDS: CCDS4487

Canonical transcript exons

ENST00000648326 — 2 exons

Exon	Start	End
ENSE00001484400	3849789	3851317
ENSE00003839986	3849373	3849486

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 90.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.8243 / max 115.8273, expressed in 1518 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
65542	4.9469	1465
65543	1.8389	1085
65544	0.0283	6
65540	0.0103	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	90.69	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.76	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.20	gold quality
prefrontal cortex	UBERON:0000451	87.82	gold quality
medial globus pallidus	UBERON:0002477	87.41	gold quality
nucleus accumbens	UBERON:0001882	87.12	gold quality
paraflocculus	UBERON:0005351	87.07	gold quality
middle frontal gyrus	UBERON:0002702	86.96	silver quality
apex of heart	UBERON:0002098	86.62	gold quality
globus pallidus	UBERON:0001875	86.36	gold quality
gastrocnemius	UBERON:0001388	86.24	gold quality
muscle of leg	UBERON:0001383	86.10	gold quality
putamen	UBERON:0001874	86.00	gold quality
frontal pole	UBERON:0002795	85.92	gold quality
tendon of biceps brachii	UBERON:0008188	85.83	gold quality
muscle organ	UBERON:0001630	85.46	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.45	gold quality
caudate nucleus	UBERON:0001873	85.42	gold quality
cerebellar cortex	UBERON:0002129	85.39	gold quality
cerebellar hemisphere	UBERON:0002245	85.39	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.32	gold quality
cerebellum	UBERON:0002037	85.05	gold quality
right frontal lobe	UBERON:0002810	85.03	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	84.92	gold quality
frontal cortex	UBERON:0001870	84.73	gold quality
heart left ventricle	UBERON:0002084	84.68	gold quality
Brodmann (1909) area 10	UBERON:0013541	84.60	gold quality
cortical plate	UBERON:0005343	84.57	gold quality
cardiac ventricle	UBERON:0002082	84.37	gold quality
neocortex	UBERON:0001950	84.34	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting FAM50B, 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-3120-5P	100.00	65.56	965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699
HSA-MIR-520D-3P	99.83	70.78	1676
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam50a	ENSDARG00000024895
mus_musculus	Fam50b	ENSMUSG00000038246
rattus_norvegicus	Fam50b	ENSRNOG00000017083
drosophila_melanogaster	CG12259	FBGN0039557
caenorhabditis_elegans		WBGENE00008143

Paralogs (1): FAM50A (ENSG00000071859)

Protein

Protein identifiers

Protein FAM50B — Q9Y247 (reviewed: Q9Y247)

Alternative names: Protein XAP-5-like

All UniProt accessions (1): Q9Y247

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Widely expressed. Mostly abundant in testis and adult and fetal brain.

Induction. Imprinted. Promoter methylation of the maternal allele may restrict expression to the paternal allele in placenta.

Similarity. Belongs to the FAM50 family.

RefSeq proteins (1): NP_036267* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007005	XAP5	Family
IPR048337	FAM50A/XAP5_C	Domain

Pfam: PF04921

UniProt features (5 total): region of interest 2, initiator methionine 1, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y247-F1	77.33	0.24

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, chr6p25, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, TSENG_IRS1_TARGETS_DN, RIZKI_TUMOR_INVASIVENESS_3D_UP, GOCC_MIDBODY, GOCC_INTERCELLULAR_BRIDGE, STEIN_ESRRA_TARGETS_UP, MARTENS_TRETINOIN_RESPONSE_UP, GHANDHI_DIRECT_IRRADIATION_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, P53_DN.V1_DN, PDGF_ERK_DN.V1_DN, GSE14415_INDUCED_VS_NATURAL_TREG_UP, DIDO1_TARGET_GENES

GO Biological Process (1): chromatin organization (GO:0006325)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), midbody (GO:0030496), intercellular bridge (GO:0045171)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cellular component organization	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1

Protein interactions and networks

STRING

508 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM50B	ZDBF2	Q9HCK1	607
FAM50B	MCTS2	A0A3B3IRV3	591
FAM50B	DIRAS3	O95661	571
FAM50B	MEST	Q5EB52	570
FAM50B	PLAGL1	Q9UM63	531
FAM50B	NAP1L5	Q96NT1	526
FAM50B	ZNF597	Q96LX8	507
FAM50B	PXDC1	Q5TGL8	505
FAM50B	RPP25L	Q8N5L8	495
FAM50B	GNAS	Q5JWF2	479
FAM50B	WDR20	Q8TBZ3	478
FAM50B	SNU13	P55769	471
FAM50B	IL17C	Q9P0M4	469
FAM50B	SNRPN	P14648	436
FAM50B	PPP1R36	Q96LQ0	435

IntAct

161 interactions, top by confidence:

A	B	Type	Score
FAM50B	LDOC1	psi-mi:“MI:0915”(physical association)	0.760
LDOC1	FAM50B	psi-mi:“MI:0915”(physical association)	0.760
FAM50B	GOLGA2	psi-mi:“MI:0915”(physical association)	0.720
GOLGA2	FAM50B	psi-mi:“MI:0915”(physical association)	0.720
FAM50B	IKZF1	psi-mi:“MI:0915”(physical association)	0.670
IKZF1	FAM50B	psi-mi:“MI:0915”(physical association)	0.670
TRIM37	FAM50B	psi-mi:“MI:0915”(physical association)	0.560
GFAP	FAM50B	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	FAM50B	psi-mi:“MI:0915”(physical association)	0.560
FAM50B	CARD9	psi-mi:“MI:0915”(physical association)	0.560
TFIP11	FAM50B	psi-mi:“MI:0915”(physical association)	0.560
FAM50B	TRIM37	psi-mi:“MI:0915”(physical association)	0.560
FAM50B	TFIP11	psi-mi:“MI:0915”(physical association)	0.560
FAM50B	GFAP	psi-mi:“MI:0915”(physical association)	0.560
FAM50B	CCDC57	psi-mi:“MI:0915”(physical association)	0.560
ACTN2	FAM50B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (70): FAM50B (Two-hybrid), FAM50B (Two-hybrid), FAM50B (Two-hybrid), FAM50B (Two-hybrid), FAM50B (Two-hybrid), CARD9 (Two-hybrid), CCDC57 (Two-hybrid), FAM50B (Two-hybrid), FAM50B (Two-hybrid), FAM50B (Two-hybrid), FAM50B (Affinity Capture-MS), FAM50B (Two-hybrid), FAM50B (Two-hybrid), FAM50B (Two-hybrid), FAM50B (Two-hybrid)

ESM2 similar proteins: A1A4P4, A1CH36, A2ALW5, A5AAL8, B0BN56, O42911, O70279, P0C2B7, P58468, P83565, Q0CLE8, Q1ECT8, Q290P4, Q2GVC2, Q3SZ86, Q4G0I0, Q4V7Q1, Q5B4U6, Q5BJW9, Q5RFR4, Q5XJW2, Q61733, Q6RUT7, Q753F1, Q7SDU5, Q7SHR9, Q80ZS3, Q86TS9, Q8BGX2, Q8BK72, Q8CHP5, Q8SPE7, Q8TAE8, Q8VD26, Q8WUQ7, Q96AN5, Q96DF8, Q9BRP8, Q9BSF4, Q9BYN8

Diamond homologs: A8WXX7, B8BDW1, Q14320, Q16U25, Q18691, Q28BK4, Q299F9, Q2VPH1, Q4KLV7, Q4R846, Q54S94, Q568K9, Q69JZ7, Q7LKZ5, Q7PYQ5, Q8H110, Q9VAY7, Q9WTJ8, Q9WV03, Q9Y247

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

62 predictions. Top by Δscore:

Variant	Effect	Δscore
6:3849787:A:AG	acceptor_gain	0.9700
6:3849788:G:GG	acceptor_gain	0.9700
6:3849788:GA:G	acceptor_gain	0.9500
6:3849783:CTGCA:C	acceptor_loss	0.9100
6:3849785:GCA:G	acceptor_loss	0.9100
6:3849786:CA:C	acceptor_loss	0.9100
6:3849787:AGAG:A	acceptor_loss	0.9100
6:3849781:T:TA	acceptor_gain	0.8600
6:3849784:T:A	acceptor_gain	0.8500
6:3849484:CAGGT:C	donor_loss	0.8400
6:3849485:AGG:A	donor_loss	0.8400
6:3849486:GGTAA:G	donor_loss	0.8400
6:3849487:G:T	donor_loss	0.8400
6:3849488:T:G	donor_loss	0.8400
6:3849788:GAGC:G	acceptor_gain	0.8400
6:3849786:CAG:C	acceptor_gain	0.8300
6:3849787:AGA:A	acceptor_gain	0.8300
6:3849788:GAG:G	acceptor_gain	0.8300
6:3849788:GAGCC:G	acceptor_gain	0.7900
6:3849489:A:AG	donor_loss	0.7600
6:3849484:C:T	donor_gain	0.7300
6:3849782:GCTGC:G	acceptor_loss	0.7200
6:3849447:C:A	donor_gain	0.7000
6:3849784:TGCAG:T	acceptor_gain	0.5700
6:3849482:GGCAG:G	donor_gain	0.4900
6:3849483:GCAGG:G	donor_gain	0.4900
6:3849483:GCAG:G	donor_gain	0.4700
6:3849490:A:AC	donor_loss	0.4300
6:3849491:G:A	donor_loss	0.4200
6:3849786:CAGAG:C	acceptor_gain	0.4100

AlphaMissense

2152 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:3850528:G:C	K239N	0.999
6:3850528:G:T	K239N	0.999
6:3850739:T:A	W310R	0.999
6:3850739:T:C	W310R	0.999
6:3850536:T:C	L242P	0.998
6:3850724:T:C	F305L	0.998
6:3850726:C:A	F305L	0.998
6:3850726:C:G	F305L	0.998
6:3850741:G:C	W310C	0.998
6:3850741:G:T	W310C	0.998
6:3850684:G:C	K291N	0.997
6:3850684:G:T	K291N	0.997
6:3850731:C:A	A307D	0.997
6:3849956:T:C	F49L	0.996
6:3849958:C:A	F49L	0.996
6:3849958:C:G	F49L	0.996
6:3850379:A:C	S190R	0.996
6:3850381:C:A	S190R	0.996
6:3850381:C:G	S190R	0.996
6:3850532:G:C	D241H	0.996
6:3850703:T:G	Y298D	0.996
6:3850740:G:C	W310S	0.996
6:3850376:T:C	F189L	0.995
6:3850378:C:A	F189L	0.995
6:3850378:C:G	F189L	0.995
6:3850382:T:G	Y191D	0.995
6:3850530:A:T	E240V	0.995
6:3850533:A:T	D241V	0.995
6:3850449:T:C	L213P	0.994
6:3850515:T:C	L235P	0.994

dbSNP variants (sampled 300 via entrez): RS1000287332 (6:3848799 G>A), RS1000325271 (6:3848488 C>T), RS1000406197 (6:3841828 T>C), RS1000478443 (6:3832022 T>A,G), RS1000575638 (6:3848576 G>A), RS1000838093 (6:3830576 T>C), RS1001036034 (6:3842374 C>T), RS1001051850 (6:3836444 C>G,T), RS1001108204 (6:3842090 A>G), RS1001140866 (6:3841646 A>G), RS1001379763 (6:3836740 A>G), RS1001656342 (6:3835904 C>T), RS1001746979 (6:3847740 G>A), RS1001888948 (6:3831668 T>C), RS1001998890 (6:3838314 T>A,C)

Disease associations

OMIM: gene MIM:614686 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001993_1	Adverse response to chemotherapy (neutropenia/leucopenia) (camptothecin)	1.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression, increases methylation	3
bisphenol A	decreases methylation, affects cotreatment, increases expression	2
Air Pollutants	affects cotreatment, increases abundance, increases expression, affects methylation	2
GSK-J4	decreases expression	1
alpha-pinene	increases expression, increases abundance, affects cotreatment	1
sodium arsenite	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
entinostat	increases expression	1
nutlin 3	affects cotreatment, increases secretion	1
bromovanin	decreases expression	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	decreases expression	1
Acrolein	increases expression, increases abundance, affects cotreatment	1
Arsenic	decreases methylation, increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	increases secretion, affects cotreatment	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ozone	affects cotreatment, increases expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Particulate Matter	affects methylation, increases abundance	1
Volatile Organic Compounds	affects cotreatment, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1WU	HAP1 FAM50B (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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