SAMD13

Summary

SAMD13 (sterile alpha motif domain containing 13, HGNC:24582) is a protein-coding gene on chromosome 1p31.1, encoding Sterile alpha motif domain-containing protein 13 (Q5VXD3).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_001134663

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24582
Approved symbol	SAMD13
Name	sterile alpha motif domain containing 13
Location	1p31.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000203943
Ensembl biotype	protein_coding
OMIM	620800
Entrez	148418

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 retained_intron

ENST00000370668, ENST00000370669, ENST00000370670, ENST00000370671, ENST00000370673, ENST00000394834, ENST00000454967, ENST00000463429, ENST00000479082

RefSeq mRNA: 3 — MANE Select: NM_001134663 NM_001010971, NM_001134663, NM_001134664

CCDS: CCDS30760, CCDS44166

Canonical transcript exons

ENST00000394834 — 4 exons

Exon	Start	End
ENSE00001453276	84301708	84301801
ENSE00001453280	84349631	84350798
ENSE00001453281	84325637	84325748
ENSE00003589303	84303203	84303287

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 89.67.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6020 / max 43.0608, expressed in 248 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
3792	0.3922	169
3791	0.2098	78

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
rectum	UBERON:0001052	89.67	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.11	gold quality
mucosa of transverse colon	UBERON:0004991	84.57	gold quality
corpus callosum	UBERON:0002336	80.24	gold quality
right testis	UBERON:0004534	79.73	gold quality
testis	UBERON:0000473	79.51	gold quality
left testis	UBERON:0004533	79.13	gold quality
transverse colon	UBERON:0001157	77.69	gold quality
hindlimb stylopod muscle	UBERON:0004252	76.26	gold quality
gastrocnemius	UBERON:0001388	75.95	gold quality
muscle of leg	UBERON:0001383	75.39	gold quality
thyroid gland	UBERON:0002046	74.30	gold quality
skeletal muscle tissue	UBERON:0001134	74.16	gold quality
adrenal tissue	UBERON:0018303	74.10	gold quality
left lobe of thyroid gland	UBERON:0001120	74.08	gold quality
right adrenal gland cortex	UBERON:0035827	73.77	gold quality
right adrenal gland	UBERON:0001233	73.61	gold quality
right uterine tube	UBERON:0001302	73.29	gold quality
right lobe of thyroid gland	UBERON:0001119	73.15	gold quality
muscle tissue	UBERON:0002385	72.72	gold quality
left adrenal gland	UBERON:0001234	72.44	gold quality
ganglionic eminence	UBERON:0004023	72.26	gold quality
fundus of stomach	UBERON:0001160	72.09	gold quality
endometrium	UBERON:0001295	72.03	gold quality
ventricular zone	UBERON:0003053	71.91	gold quality
adrenal gland	UBERON:0002369	71.88	gold quality
left adrenal gland cortex	UBERON:0035825	71.85	gold quality
duodenum	UBERON:0002114	71.73	gold quality
body of stomach	UBERON:0001161	71.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting SAMD13, 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-190A-3P	100.00	80.35	5520
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4659A-3P	99.80	72.62	4248

Literature-anchored findings (GeneRIF, showing 1)

• SAMD13 serves as a useful prognostic biomarker for hepatocellular carcinoma. (PMID:37968735)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Samd13	ENSMUSG00000048652
rattus_norvegicus	Samd13	ENSRNOG00000016432
drosophila_melanogaster	Sfmbt	FBGN0032475
caenorhabditis_elegans	lin-61	WBGENE00003041
caenorhabditis_elegans	mbtr-1	WBGENE00021661

Paralogs (18): SCMH1 (ENSG00000010803), MBTD1 (ENSG00000011258), SCML1 (ENSG00000047634), L3MBTL2 (ENSG00000100395), SCML2 (ENSG00000102098), PHC1 (ENSG00000111752), THAP10 (ENSG00000129028), PHC2 (ENSG00000134686), SAMD1 (ENSG00000141858), SCML4 (ENSG00000146285), L3MBTL4 (ENSG00000154655), SFMBT1 (ENSG00000163935), PHC3 (ENSG00000173889), L3MBTL1 (ENSG00000185513), SAMD7 (ENSG00000187033), SAMD11 (ENSG00000187634), SFMBT2 (ENSG00000198879), L3MBTL3 (ENSG00000198945)

Protein

Protein identifiers

Sterile alpha motif domain-containing protein 13 — Q5VXD3 (reviewed: Q5VXD3)

All UniProt accessions (2): Q5VXD3, H7BZX5

Isoforms (4)

UniProt ID	Names	Canonical?
Q5VXD3-1	1	yes
Q5VXD3-2	2
Q5VXD3-3	3
Q5VXD3-4	4

RefSeq proteins (3): NP_001010971, NP_001128135, NP_001128136 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001660	SAM	Domain
IPR013761	SAM/pointed_sf	Homologous_superfamily
IPR050548	PcG_chromatin_remod_factors	Family

Pfam: PF00536

UniProt features (5 total): splice variant 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VXD3-F1	78.42	0.53

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, MARSON_BOUND_BY_FOXP3_STIMULATED, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP, STK33_NOMO_DN, DLX6_TARGET_GENES, FEV_TARGET_GENES, LHX9_TARGET_GENES, PRDM5_TARGET_GENES, ZFP91_TARGET_GENES, ZNF410_TARGET_GENES

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

682 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SAMD13	REP15	Q6BDI9	506
SAMD13	NXPE4	Q6UWF7	506
SAMD13	TINAG	Q9UJW2	417
SAMD13	SAMD12	Q8N8I0	403
SAMD13	SPRR2G	Q9BYE4	398
SAMD13	PJA2	O43164	356
SAMD13	TMEM97	Q5BJF2	354
SAMD13	THSD4	Q6ZMP0	336
SAMD13	KLF12	Q9Y4X4	334
SAMD13	CAMK2N1	Q7Z7J9	322
SAMD13	STPG2	Q8N412	320
SAMD13	NXPH2	O95156	318
SAMD13	HIVEP2	P31629	299
SAMD13	ESRP2	Q9H6T0	290
SAMD13	GAS7	O60861	287

IntAct

4 interactions, top by confidence:

A	B	Type	Score
L3MBTL3	SAMD13	psi-mi:“MI:0914”(association)	0.640
L3MBTL3	P4HA1	psi-mi:“MI:0914”(association)	0.530

BioGRID (8): SAMD13 (Affinity Capture-MS), SAMD13 (Affinity Capture-RNA), SAMD13 (Affinity Capture-MS), SAMD13 (Affinity Capture-MS), SAMD13 (Affinity Capture-MS), SAMD13 (Affinity Capture-MS), SAMD13 (Affinity Capture-MS), SAMD13 (Affinity Capture-MS)

ESM2 similar proteins: A2ALK8, A4D7T3, A8XWC4, D3YUG0, F1LYQ8, F1M386, F1MSG6, F1P065, F1PBJ0, F1QWA8, F8VPU2, G5EDB9, O14830, O15068, O45818, P0CE43, P11346, P19686, P26045, P33402, P54936, P70600, P97874, Q02108, Q07DZ7, Q14289, Q4ZHS0, Q5DU57, Q5FVC7, Q5RAB8, Q5VXD3, Q5ZK62, Q63406, Q64096, Q6AYC5, Q6ZQK5, Q811M1, Q86YR7, Q8CHG7, Q8K3X6

Diamond homologs: A2A5N8, B1B1A0, D3YUG0, D3YXK1, D3ZWK4, E1C2V1, O02274, O60284, O95251, P39769, P59178, P70047, P70475, P78364, P97500, Q01538, Q05BQ5, Q1JQD9, Q1RNF8, Q29L50, Q32N90, Q3MIF2, Q4V7W5, Q5DTW2, Q5R737, Q5SVQ0, Q5VUG0, Q5VXD3, Q64028, Q6DIN3, Q6P5G3, Q6SPE9, Q6SPF0, Q7Z3H4, Q80TY4, Q810T5, Q8BLB7, Q8C8Y5, Q8CFC2, Q8CHP6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

887 predictions. Top by Δscore:

Variant	Effect	Δscore
1:84311654:GCA:G	donor_gain	1.0000
1:84311657:G:GG	donor_gain	1.0000
1:84298563:GGGAG:G	donor_gain	0.9900
1:84298564:GGAG:G	donor_gain	0.9900
1:84298564:GGAGG:G	donor_gain	0.9900
1:84298565:GAG:G	donor_gain	0.9900
1:84298565:GAGG:G	donor_gain	0.9900
1:84298565:GAGGT:G	donor_loss	0.9900
1:84298566:AGGT:A	donor_loss	0.9900
1:84298568:GTA:G	donor_loss	0.9900
1:84298569:TAAG:T	donor_loss	0.9900
1:84308918:T:G	donor_gain	0.9900
1:84325635:A:AG	acceptor_gain	0.9900
1:84325636:G:GG	acceptor_gain	0.9900
1:84325636:GTTCC:G	acceptor_gain	0.9900
1:84298568:G:GG	donor_gain	0.9800
1:84303201:A:AG	acceptor_gain	0.9800
1:84303202:G:GG	acceptor_gain	0.9800
1:84323053:G:GT	donor_gain	0.9700
1:84325636:GTT:G	acceptor_gain	0.9700
1:84325744:AACAG:A	donor_loss	0.9700
1:84325745:ACAGG:A	donor_loss	0.9700
1:84325746:CAGGT:C	donor_loss	0.9700
1:84325747:AG:A	donor_loss	0.9700
1:84325748:GG:G	donor_loss	0.9700
1:84325749:GT:G	donor_loss	0.9700
1:84325750:T:TC	donor_loss	0.9700
1:84325751:A:C	donor_loss	0.9700
1:84349625:TTATA:T	acceptor_loss	0.9700
1:84349626:TATA:T	acceptor_loss	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000053283 (1:84343249 G>A), RS1000079386 (1:84298834 G>A), RS1000103767 (1:84343013 A>G), RS1000181497 (1:84297521 T>A), RS1000196268 (1:84316843 A>G), RS1000200802 (1:84313042 A>G), RS1000302317 (1:84336796 A>G), RS1000377950 (1:84330038 A>G), RS1000451446 (1:84299039 C>T), RS1000469680 (1:84329187 A>G), RS1000491506 (1:84318549 T>C), RS1000529760 (1:84350666 T>C), RS1000547445 (1:84309997 TAAAC>T), RS1000643081 (1:84325290 G>A), RS1000658448 (1:84332014 T>A,C,G)

Disease associations

OMIM: gene MIM:620800 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001762_637	Obesity-related traits	4.000000e-06
GCST009391_1061	Metabolite levels	3.000000e-07
GCST010039_17	Adverse response to inhaled corticosteroid treatment x age interaction in asthma	4.000000e-07
GCST011768_20	Schizophrenia	9.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010364	lysophosphatidylcholine 20:5 measurement
EFO:0008007	age at assessment

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	5
methylmercuric chloride	decreases expression	2
trichostatin A	increases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
(+)-JQ1 compound	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Silicon Dioxide	decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
bisphenol A	decreases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
butyraldehyde	decreases expression	1
avobenzone	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression, affects cotreatment	1
Vorinostat	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Calcitriol	decreases expression, affects cotreatment	1
Carbamazepine	affects expression	1
Catechin	affects cotreatment, decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, decreases expression	1
Formaldehyde	decreases expression	1
Testosterone	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases methylation	1
Gold Compounds	decreases expression	1

Clinical trials (associated diseases)

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