SAMD4B

gene
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Also known as FLJ10211MGC99832SMGBhSmaug2

Summary

SAMD4B (sterile alpha motif domain containing 4B, HGNC:25492) is a protein-coding gene on chromosome 19q13.2, encoding Protein Smaug homolog 2 (Q5PRF9). Has transcriptional repressor activity. It is a selective cancer dependency (DepMap: 21.3% of cell lines).

Enables RNA binding activity. Predicted to be involved in nuclear-transcribed mRNA poly(A) tail shortening. Predicted to act upstream of or within cerebellar neuron development. Located in cytosol.

Source: NCBI Gene 55095 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 98 total
  • Cancer dependency (DepMap): dependent in 21.3% of screened cell lines
  • MANE Select transcript: NM_001384574

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25492
Approved symbolSAMD4B
Namesterile alpha motif domain containing 4B
Location19q13.2
Locus typegene with protein product
StatusApproved
AliasesFLJ10211, MGC99832, SMGB, hSmaug2
Ensembl geneENSG00000179134
Ensembl biotypeprotein_coding
OMIM619231
Entrez55095

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 16 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000314471, ENST00000594204, ENST00000595476, ENST00000596271, ENST00000596319, ENST00000596368, ENST00000598605, ENST00000598913, ENST00000599712, ENST00000600018, ENST00000601613, ENST00000610417, ENST00000863006, ENST00000863007, ENST00000863008, ENST00000863009, ENST00000936210, ENST00000936211, ENST00000936212, ENST00000936213, ENST00000961383

RefSeq mRNA: 30 — MANE Select: NM_001384574 NM_001303614, NM_001384565, NM_001384566, NM_001384568, NM_001384569, NM_001384570, NM_001384571, NM_001384573, NM_001384574, NM_001384575, NM_001384576, NM_001384577, NM_001384578, NM_001384580, NM_001384581, NM_001384582, NM_001384583, NM_001384584, NM_001384585, NM_001384586, NM_001384587, NM_001384588, NM_001384589, NM_001384590, NM_001384591, NM_001384592, NM_001384593, NM_001384594, NM_001384595, NM_018028

CCDS: CCDS33020, CCDS77295

Canonical transcript exons

ENST00000610417 — 14 exons

ExonStartEnd
ENSE000003416703936965539370125
ENSE000007054623937565039375889
ENSE000011415083935668939357089
ENSE000012334883937850439378589
ENSE000012334943937748539377824
ENSE000012335103937670539376791
ENSE000015106053935400639354066
ENSE000024451103938320839383291
ENSE000025041393938099039381113
ENSE000031945603934242139342576
ENSE000034853003937996639380084
ENSE000036631943938058739380785
ENSE000037164313938349939385700
ENSE000037898563937643739376546

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 99.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.9176 / max 148.7481, expressed in 1789 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
17569812.85971783
1756991.0579694

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583499.03gold quality
adenohypophysisUBERON:000219698.56gold quality
tibial nerveUBERON:000132398.51gold quality
C1 segment of cervical spinal cordUBERON:000646998.46gold quality
right frontal lobeUBERON:000281098.37gold quality
ectocervixUBERON:001224998.27gold quality
mucosa of stomachUBERON:000119998.26gold quality
left ovaryUBERON:000211998.26gold quality
esophagogastric junction muscularis propriaUBERON:003584198.11gold quality
endocervixUBERON:000045898.09gold quality
right ovaryUBERON:000211898.05gold quality
anterior cingulate cortexUBERON:000983598.03gold quality
lower esophagusUBERON:001347398.03gold quality
lower esophagus muscularis layerUBERON:003583398.03gold quality
skin of legUBERON:000151198.00gold quality
cingulate cortexUBERON:000302798.00gold quality
right testisUBERON:000453497.96gold quality
left lobe of thyroid glandUBERON:000112097.88gold quality
right lobe of thyroid glandUBERON:000111997.87gold quality
left uterine tubeUBERON:000130397.86gold quality
left testisUBERON:000453397.83gold quality
popliteal arteryUBERON:000225097.82gold quality
tibial arteryUBERON:000761097.82gold quality
skin of abdomenUBERON:000141697.81gold quality
body of uterusUBERON:000985397.77gold quality
pituitary glandUBERON:000000797.74gold quality
right uterine tubeUBERON:000130297.74gold quality
amygdalaUBERON:000187697.72gold quality
muscle layer of sigmoid colonUBERON:003580597.70gold quality
right coronary arteryUBERON:000162597.67gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-ANND-3yes10.23
E-GEOD-137537yes3.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

168 targeting SAMD4B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4533100.0069.482758
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-4283100.0066.422097
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-211099.9666.681930
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-568899.9673.234504
HSA-MIR-185-3P99.9567.011743
HSA-MIR-391099.9571.132227
HSA-MIR-314399.9371.963104
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-427199.8868.322244

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 21.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Results suggest that SAMD4B is a widely expressed gene involved in AP-1-, p53-and p21-mediated transcriptional signaling activity. (PMID:20510020)
  • miR451 suppresses the malignant characteristics of colorectal cancer via targeting SAMD4B. (PMID:34109425)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioSAMD4BENSDARG00000086735
mus_musculusSamd4bENSMUSG00000109336
rattus_norvegicusSamd4bENSRNOG00000079475
drosophila_melanogastersmgFBGN0016070
caenorhabditis_elegansWBGENE00022538

Paralogs (1): SAMD4A (ENSG00000020577)

Protein

Protein identifiers

Protein Smaug homolog 2Q5PRF9 (reviewed: Q5PRF9)

Alternative names: Sterile alpha motif domain-containing protein 4B

All UniProt accessions (6): Q5PRF9, M0QX45, M0QY61, M0QZ22, M0QZW7, M0R0X3

UniProt curated annotations — full annotation on UniProt →

Function. Has transcriptional repressor activity. Overexpression inhibits the transcriptional activities of AP-1, p53/TP53 and CDKN1A.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Widely expressed in embryonic and adult tissues.

Similarity. Belongs to the SMAUG family.

RefSeq proteins (30): NP_001290543, NP_001371494, NP_001371495, NP_001371497, NP_001371498, NP_001371499, NP_001371500, NP_001371502, NP_001371503, NP_001371504, NP_001371505, NP_001371506, NP_001371507, NP_001371509, NP_001371510, NP_001371511, NP_001371512, NP_001371513, NP_001371514, NP_001371515, NP_001371516, NP_001371517, NP_001371518, NP_001371519, NP_001371520, NP_001371521, NP_001371522, NP_001371523, NP_001371524, NP_060498 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001660SAMDomain
IPR013761SAM/pointed_sfHomologous_superfamily
IPR037093PHAT_dom_sfHomologous_superfamily
IPR037634Smaug_SAMDomain
IPR050897SMAUG/VTS1_RNA-bindFamily
IPR058599PHAT_Smg/ZCCHC2-likeDomain

Pfam: PF00536, PF26034

UniProt features (25 total): modified residue 13, compositionally biased region 7, region of interest 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5PRF9-F165.470.36

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 (13): 172, 271, 278, 279, 281, 407, 555, 557, 563, 592, 600, 602, 628

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 193 (showing top): GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_TRANSLATION, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSLATION_REGULATOR_ACTIVITY, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GCM_NUMA1, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_DEADENYLATION_DEPENDENT_DECAY, KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION, GOBP_NUCLEAR_TRANSCRIBED_MRNA_POLY_A_TAIL_SHORTENING, GCM_NF2, CCCAGAG_MIR326

GO Biological Process (3): nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289), negative regulation of translation (GO:0017148), regulation of mRNA stability (GO:0043488)

GO Molecular Function (4): RNA binding (GO:0003723), mRNA binding (GO:0003729), translation repressor activity (GO:0030371), protein binding (GO:0005515)

GO Cellular Component (4): P-body (GO:0000932), nucleus (GO:0005634), cytosol (GO:0005829), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay1
nuclear-transcribed mRNA catabolic process1
translation1
regulation of translation1
negative regulation of gene expression1
negative regulation of protein metabolic process1
regulation of RNA stability1
regulation of mRNA catabolic process1
nucleic acid binding1
RNA binding1
negative regulation of translation1
translation regulator activity1
binding1
cytoplasmic ribonucleoprotein granule1
intracellular membrane-bounded organelle1
cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

1050 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SAMD4BNANOS1Q8WY41722
SAMD4BEIF4ENIF1Q9NRA8580
SAMD4BUSH1GQ495M9494
SAMD4BANK2Q01484490
SAMD4BANK1P16157470
SAMD4BANK3Q12955470
SAMD4BCEBPZOSA8MTT3453
SAMD4BE9PNW1E9PNW1425
SAMD4BGOLGA3Q08378409
SAMD4BTMEM63CQ9P1W3406
SAMD4BWDR5BQ86VZ2406
SAMD4BRNPC3Q96LT9396
SAMD4BPUM2Q8TB72380
SAMD4BC1QTNF12Q5T7M4378
SAMD4BCAPN9O14815375

IntAct

74 interactions, top by confidence:

ABTypeScore
SAMD4BYWHAQpsi-mi:“MI:0914”(association)0.850
SAMD4BYWHAGpsi-mi:“MI:0914”(association)0.840
YWHAQWDR62psi-mi:“MI:0914”(association)0.830
SAMD4BYWHAZpsi-mi:“MI:0915”(physical association)0.760
SAMD4BYWHAEpsi-mi:“MI:0915”(physical association)0.740
YWHAGBLTP3Bpsi-mi:“MI:0914”(association)0.640
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
YWHABBLTP3Bpsi-mi:“MI:0914”(association)0.610
YWHAHBLTP3Bpsi-mi:“MI:0914”(association)0.570
LRRC8ESAMD4Bpsi-mi:“MI:0915”(physical association)0.560
CCDC179SAMD4Bpsi-mi:“MI:0915”(physical association)0.560
SAMD4Bpsi-mi:“MI:0915”(physical association)0.560
SAMD4BUSP53psi-mi:“MI:0915”(physical association)0.560
SAMD4BBCL2L10psi-mi:“MI:0915”(physical association)0.560
SAMD4BRSRC2psi-mi:“MI:0915”(physical association)0.560
SAMD4BLRRC8Epsi-mi:“MI:0915”(physical association)0.560
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
YWHAQIGLC7psi-mi:“MI:0914”(association)0.530
YWHABSHTN1psi-mi:“MI:0914”(association)0.530
YWHAZBLTP3Bpsi-mi:“MI:0914”(association)0.530
YWHABPLEKHG3psi-mi:“MI:0914”(association)0.480
YWHAQPLEKHG3psi-mi:“MI:0914”(association)0.480
SFNSAMD4Bpsi-mi:“MI:0915”(physical association)0.400
SAMD4BCFTRpsi-mi:“MI:0915”(physical association)0.370
RGMABDP1psi-mi:“MI:0914”(association)0.350
NfycBDP1psi-mi:“MI:0914”(association)0.350

BioGRID (178): SAMD4B (Synthetic Growth Defect), SAMD4B (Proximity Label-MS), SAMD4B (Proximity Label-MS), SAMD4B (Proximity Label-MS), SAMD4B (Proximity Label-MS), SAMD4B (Affinity Capture-MS), SAMD4B (Affinity Capture-MS), SAMD4B (Affinity Capture-MS), SAMD4B (Affinity Capture-MS), SAMD4A (Affinity Capture-MS), PDP1 (Affinity Capture-MS), YWHAG (Affinity Capture-MS), YWHAE (Affinity Capture-MS), ACTA2 (Affinity Capture-MS), YWHAZ (Affinity Capture-MS)

ESM2 similar proteins: A0JNT9, A0JPP8, A1X157, O15169, O75145, O75335, P39880, P60469, Q07DZ5, Q08CF3, Q08E13, Q09YM8, Q2M1P5, Q2QLG9, Q2VUH7, Q32PN7, Q3TMW1, Q3UHC7, Q3UIL6, Q3UIW5, Q3UJV1, Q5DU25, Q5FWS6, Q5JU85, Q5PRF9, Q5XI59, Q5ZJ07, Q674X7, Q68UI8, Q69ZS8, Q6IPM2, Q6NZT2, Q6P402, Q6P730, Q6ZP65, Q80XS6, Q80Y83, Q8JZP9, Q8K1S6, Q8R4R9

Diamond homologs: B3NFQ7, B4HKJ7, B4QMP1, B5DF21, P60320, Q0IHW3, Q23972, Q4P965, Q4WJS2, Q5BGC4, Q5FWP2, Q5PRF9, Q6CHK0, Q758Y4, Q7RZQ3, Q80XS6, Q8CBY1, Q95LV5, Q9UPU9, J9VVN9, Q08831, Q5AI80, Q6BSL1, Q6CY29, Q6FM94, Q9P6R7, Q4IBN1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 56 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Activation of BAD and translocation to mitochondria7130.0×4e-12
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex7114.7×6e-12
SARS-CoV-1 targets host intracellular signalling and regulatory pathways7114.7×6e-12
Activation of BH3-only proteins784.8×6e-11
RHO GTPases activate PKNs754.2×2e-09
Intrinsic Pathway for Apoptosis750.0×3e-09
FOXO-mediated transcription541.0×2e-06
SARS-CoV-1-host interactions730.0×9e-08

GO biological processes:

GO termPartnersFoldFDR
protein targeting537.4×5e-05
intracellular protein localization919.2×4e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance82
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2409 predictions. Top by Δscore:

VariantEffectΔscore
19:39342574:GCG:Gdonor_gain1.0000
19:39342574:GCGGT:Gdonor_loss1.0000
19:39342575:CGGTG:Cdonor_loss1.0000
19:39342577:G:GGdonor_gain1.0000
19:39342578:T:Gdonor_loss1.0000
19:39357086:GCTG:Gdonor_gain1.0000
19:39357088:TGGTG:Tdonor_loss1.0000
19:39357089:GGTG:Gdonor_loss1.0000
19:39357090:G:Adonor_loss1.0000
19:39357090:G:GGdonor_gain1.0000
19:39357091:TGA:Tdonor_loss1.0000
19:39357092:GAG:Gdonor_loss1.0000
19:39369652:TAGC:Tacceptor_loss1.0000
19:39369653:A:AGacceptor_gain1.0000
19:39369653:AGCC:Aacceptor_loss1.0000
19:39369654:G:GGacceptor_gain1.0000
19:39369654:GC:Gacceptor_gain1.0000
19:39369654:GCC:Gacceptor_gain1.0000
19:39369654:GCCA:Gacceptor_gain1.0000
19:39369976:A:Gdonor_gain1.0000
19:39376429:T:TAacceptor_gain1.0000
19:39376434:A:Gacceptor_gain1.0000
19:39376436:GAT:Gacceptor_gain1.0000
19:39376436:GATGT:Gacceptor_gain1.0000
19:39376543:TCAGG:Tdonor_loss1.0000
19:39376545:AGGTG:Adonor_loss1.0000
19:39376546:GG:Gdonor_loss1.0000
19:39376547:GTG:Gdonor_loss1.0000
19:39376548:T:Gdonor_loss1.0000
19:39376570:G:Tdonor_gain1.0000

AlphaMissense

4492 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:39356900:T:CF3L1.000
19:39356902:C:AF3L1.000
19:39356902:C:GF3L1.000
19:39356942:T:AW17R1.000
19:39356942:T:CW17R1.000
19:39356956:G:CE21D1.000
19:39356956:G:TE21D1.000
19:39356958:A:CQ22P1.000
19:39356967:C:AA25D1.000
19:39356970:T:CL26P1.000
19:39356973:T:CL27P1.000
19:39356979:T:CL29P1.000
19:39356982:T:CL30P1.000
19:39357011:T:CF40L1.000
19:39357012:T:CF40S1.000
19:39357013:C:AF40L1.000
19:39357013:C:GF40L1.000
19:39357015:T:CL41P1.000
19:39357027:T:CL45P1.000
19:39357078:C:AA62D1.000
19:39369706:T:CL83P1.000
19:39369718:T:AL87H1.000
19:39369718:T:CL87P1.000
19:39369724:T:CL89P1.000
19:39369727:T:AL90H1.000
19:39369727:T:CL90P1.000
19:39369759:T:CY101H1.000
19:39369759:T:GY101D1.000
19:39369772:T:CL105P1.000
19:39369784:T:CL109P1.000

dbSNP variants (sampled 300 via entrez): RS1000004715 (19:39387518 C>T), RS1000143167 (19:39352860 C>T), RS1000161518 (19:39351359 C>T), RS1000213780 (19:39375509 G>T), RS1000288087 (19:39368780 A>G), RS1000291759 (19:39381981 G>A), RS1000366314 (19:39363801 G>C), RS1000452786 (19:39352632 C>T), RS1000536828 (19:39387971 CTA>C), RS1000624244 (19:39383439 C>T), RS1000655322 (19:39383748 G>A), RS1000714486 (19:39352763 G>C,T), RS1000777245 (19:39358942 T>C), RS1000799107 (19:39341379 C>T), RS1000812754 (19:39376936 G>C)

Disease associations

OMIM: gene MIM:619231 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001762_907Obesity-related traits6.000000e-06
GCST011352_11Alanine aminotransferase levels2.000000e-12

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0003940physical activity

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophenincreases expression, decreases expression3
Air Pollutantsaffects expression, increases abundance, increases expression2
FR900359affects phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
sodium arseniteincreases expression1
cobaltous chlorideincreases expression1
coumarinaffects phosphorylation1
di-n-butylphosphoric acidaffects expression1
ICG 001decreases expression1
abrineincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Caffeineaffects phosphorylation1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ozoneaffects expression, increases abundance1
Potassium Dichromatedecreases expression1
Quercetinincreases phosphorylation1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Tetrachlorodibenzodioxinaffects expression1
Dronabinolincreases expression1
Tobacco Smoke Pollutionincreases expression1
Ursodeoxycholic Acidaffects expression1
Aflatoxin B1decreases methylation1
Gold Compoundsincreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.