SAMD10

Summary

SAMD10 (sterile alpha motif domain containing 10, HGNC:16129) is a protein-coding gene on chromosome 20q13.33, encoding Sterile alpha motif domain-containing protein 10 (Q9BYL1).

Predicted to be involved in cell surface receptor protein tyrosine kinase signaling pathway. Predicted to be active in cytoplasmic side of plasma membrane.

Source: NCBI Gene 140700 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_080621

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16129
Approved symbol	SAMD10
Name	sterile alpha motif domain containing 10
Location	20q13.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000130590
Ensembl biotype	protein_coding
Entrez	140700

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000369886, ENST00000450107, ENST00000478694, ENST00000498830

RefSeq mRNA: 1 — MANE Select: NM_080621 NM_080621

CCDS: CCDS13549

Canonical transcript exons

ENST00000369886 — 5 exons

Exon	Start	End
ENSE00000991845	63979377	63979642
ENSE00001703927	63974116	63975532
ENSE00003650875	63976971	63977142
ENSE00003665291	63977225	63977406
ENSE00003673642	63975692	63975832

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 90.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.7407 / max 27.8766, expressed in 1002 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
188442	1.6075	744
188444	0.7618	355
188441	0.2916	169
188443	0.0798	45

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	90.87	gold quality
cerebellar hemisphere	UBERON:0002245	90.38	gold quality
cerebellar cortex	UBERON:0002129	90.19	gold quality
cerebellum	UBERON:0002037	89.11	gold quality
cortical plate	UBERON:0005343	87.50	gold quality
lower esophagus mucosa	UBERON:0035834	86.68	gold quality
gingival epithelium	UBERON:0001949	86.46	gold quality
nucleus accumbens	UBERON:0001882	85.65	gold quality
right uterine tube	UBERON:0001302	84.53	gold quality
vena cava	UBERON:0004087	84.29	gold quality
putamen	UBERON:0001874	83.84	gold quality
gingiva	UBERON:0001828	83.43	gold quality
granulocyte	CL:0000094	83.36	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	83.29	gold quality
nasal cavity epithelium	UBERON:0005384	83.24	gold quality
thymus	UBERON:0002370	82.61	silver quality
caudate nucleus	UBERON:0001873	82.48	gold quality
esophagus mucosa	UBERON:0002469	82.15	gold quality
apex of heart	UBERON:0002098	82.05	gold quality
vastus lateralis	UBERON:0001379	81.13	gold quality
buccal mucosa cell	CL:0002336	81.08	gold quality
right frontal lobe	UBERON:0002810	80.83	gold quality
quadriceps femoris	UBERON:0001377	80.70	gold quality
cortex of kidney	UBERON:0001225	80.66	gold quality
ganglionic eminence	UBERON:0004023	80.60	gold quality
cardia of stomach	UBERON:0001162	80.36	gold quality
metanephros cortex	UBERON:0010533	80.15	gold quality
subthalamic nucleus	UBERON:0001906	79.64	gold quality
lymph node	UBERON:0000029	79.56	gold quality
lateral globus pallidus	UBERON:0002476	79.21	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting SAMD10, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	samd10a	ENSDARG00000079978
danio_rerio	samd10b	ENSDARG00000094377
mus_musculus	Samd10	ENSMUSG00000038605
rattus_norvegicus	Samd10	ENSRNOG00000036719
drosophila_melanogaster	ave	FBGN0050476
caenorhabditis_elegans		WBGENE00044341

Paralogs (1): SAMD12 (ENSG00000177570)

Protein

Protein identifiers

Sterile alpha motif domain-containing protein 10 — Q9BYL1 (reviewed: Q9BYL1)

All UniProt accessions (2): Q9BYL1, Q5JWV3

RefSeq proteins (1): NP_542188* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001660	SAM	Domain
IPR013761	SAM/pointed_sf	Homologous_superfamily
IPR039144	Aveugle-like_SAM_dom	Domain
IPR052268	SAM_domain-containing_protein	Family

Pfam: PF07647

UniProt features (2 total): chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BYL1-F1	68.05	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 87 (showing top): RNGTGGGC_UNKNOWN, GCANCTGNY_MYOD_Q6, OZEN_MIR125B1_TARGETS, GOCC_CYTOPLASMIC_SIDE_OF_MEMBRANE, GOCC_SIDE_OF_MEMBRANE, GOBP_CELL_SURFACE_RECEPTOR_PROTEIN_TYROSINE_KINASE_SIGNALING_PATHWAY, SCGGAAGY_ELK1_02, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, MEISSNER_NPC_HCP_WITH_H3K4ME2, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP, EGR_Q6, E2F1_UP.V1_DN, RB_P107_DN.V1_UP, GOBP_ENZYME_LINKED_RECEPTOR_PROTEIN_SIGNALING_PATHWAY, NRF1_Q6

GO Biological Process (1): cell surface receptor protein tyrosine kinase signaling pathway (GO:0007169)

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

GO Cellular Component (1): cytoplasmic side of plasma membrane (GO:0009898)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
enzyme-linked receptor protein signaling pathway	1
binding	1
plasma membrane	1
cytoplasmic side of membrane	1

Protein interactions and networks

STRING

328 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SAMD10	AVPI1	Q5T686	570
SAMD10	ALKBH7	Q9BT30	530
SAMD10	SAMD14	Q8IZD0	518
SAMD10	SAMD5	Q5TGI4	516
SAMD10	CLLU1-AS1	Q5K130	507
SAMD10	NCKIPSD	Q9NZQ3	504
SAMD10	DRC7	Q8IY82	456
SAMD10	PIGP	P57054	450
SAMD10	SLFN5	Q08AF3	446
SAMD10	ZNF880	Q6PDB4	418
SAMD10	METTL27	Q8N6F8	416
SAMD10	CCDC126	Q96EE4	416
SAMD10	SAMD7	Q7Z3H4	410
SAMD10	NHSL2	Q5HYW2	406
SAMD10	C2orf69	Q8N8R5	398

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CNKSR3	COLGALT2	psi-mi:“MI:0914”(association)	0.530
CNKSR3	AZGP1	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): SAMD10 (Affinity Capture-MS), SAMD10 (Affinity Capture-MS)

ESM2 similar proteins: A2AKB9, A2AWP8, A4FV57, D3YYI7, G3V9M2, O09112, O43189, O60347, O77638, O94827, O95644, P20749, P22681, P22682, P30291, P49797, P98201, Q01201, Q04863, Q09YL6, Q0GA42, Q13202, Q13387, Q3TZ87, Q3UR85, Q3V1H9, Q5XI70, Q66T02, Q6A039, Q6RFZ7, Q6ZN18, Q70EL4, Q7Z6J2, Q86YJ5, Q8BUM9, Q8CE64, Q8N554, Q8N6N2, Q8R4T5, Q8TC41

Diamond homologs: Q0VE29, Q5RDW3, Q7TST3, Q8ML92, Q8N8I0, Q9BYL1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1079 predictions. Top by Δscore:

Variant	Effect	Δscore
20:63975828:CCGGC:C	acceptor_gain	1.0000
20:63975829:CGGC:C	acceptor_gain	1.0000
20:63975829:CGGCC:C	acceptor_gain	1.0000
20:63975830:GGC:G	acceptor_gain	1.0000
20:63975831:GC:G	acceptor_gain	1.0000
20:63975831:GCC:G	acceptor_loss	1.0000
20:63975832:CC:C	acceptor_gain	1.0000
20:63975833:C:CA	acceptor_loss	1.0000
20:63975833:C:CC	acceptor_gain	1.0000
20:63975833:C:T	acceptor_gain	1.0000
20:63975834:T:A	acceptor_loss	1.0000
20:63975834:T:C	acceptor_loss	1.0000
20:63976967:GTACC:G	donor_loss	1.0000
20:63976968:TA:T	donor_loss	1.0000
20:63976969:A:AC	donor_gain	1.0000
20:63976970:C:CA	donor_loss	1.0000
20:63976970:C:CC	donor_gain	1.0000
20:63975760:T:TA	donor_gain	0.9900
20:63976944:C:CA	donor_gain	0.9900
20:63977103:T:C	acceptor_gain	0.9900
20:63977138:CGGCC:C	acceptor_gain	0.9900
20:63977143:C:CC	acceptor_gain	0.9900
20:63977143:C:G	acceptor_loss	0.9900
20:63977144:T:A	acceptor_loss	0.9900
20:63979371:GCTCA:G	donor_loss	0.9900
20:63979372:CTCA:C	donor_loss	0.9900
20:63979373:TCACC:T	donor_loss	0.9900
20:63979374:CACC:C	donor_loss	0.9900
20:63979375:A:C	donor_loss	0.9900
20:63979375:ACCGT:A	donor_gain	0.9900

AlphaMissense

1297 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:63975832:C:T	G149D	0.998
20:63976976:A:T	I147N	0.998
20:63977036:A:G	L127P	0.998
20:63977040:A:G	W126R	0.998
20:63977040:A:T	W126R	0.998
20:63977048:A:T	V123D	0.998
20:63977064:A:G	W118R	0.998
20:63977064:A:T	W118R	0.998
20:63975799:A:G	L160P	0.997
20:63975823:A:G	L152P	0.997
20:63976971:C:G	G149R	0.997
20:63976976:A:C	I147S	0.997
20:63975814:A:G	L155P	0.996
20:63976976:A:G	I147T	0.996
20:63976991:A:G	F142S	0.996
20:63977036:A:T	L127H	0.996
20:63977038:C:A	W126C	0.996
20:63977038:C:G	W126C	0.996
20:63977062:C:A	W118C	0.996
20:63977062:C:G	W118C	0.996
20:63975823:A:T	L152Q	0.995
20:63975832:C:A	G149V	0.995
20:63976971:C:A	G149C	0.995
20:63976990:G:C	F142L	0.994
20:63976990:G:T	F142L	0.994
20:63976992:A:G	F142L	0.994
20:63975736:A:G	L181P	0.993
20:63975823:A:C	L152R	0.993
20:63975799:A:C	L160R	0.992
20:63975799:A:T	L160Q	0.992

dbSNP variants (sampled 300 via entrez): RS1000352145 (20:63976539 G>C,T), RS1000426349 (20:63982126 A>G), RS1000532003 (20:63974362 G>A), RS1000601950 (20:63975632 C>A), RS1000862131 (20:63981885 G>T), RS1000969561 (20:63974750 A>C), RS1000974025 (20:63980528 C>A), RS1001080458 (20:63980954 A>C,G), RS1001499958 (20:63976503 C>G,T), RS1001597235 (20:63976229 A>G), RS1001699059 (20:63975359 G>A,T), RS1002019658 (20:63980357 G>C,T), RS1002065512 (20:63974235 G>T), RS1002303874 (20:63980381 C>A,G,T), RS1002870031 (20:63979582 C>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

5 associations (top):

Study	Trait	p-value
GCST001942_22	Prostate cancer	4.000000e-16
GCST003995_29	Tonsillectomy	8.000000e-09
GCST005014_163	Tonsillectomy	8.000000e-09
GCST007001_16	Cerebrospinal AB1-42 levels in normal cognition	3.000000e-07
GCST90011900_13	Serum alkaline phosphatase levels	5.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007924	tonsillectomy risk measurement
EFO:0004670	beta-amyloid 1-42 measurement
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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression	2
(+)-JQ1 compound	decreases expression	2
Cadmium Chloride	decreases expression, increases expression	2
GSK-J4	decreases expression	1
dicrotophos	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
Bortezomib	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases methylation	1
Acrylamide	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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