SMKR1

Summary

SMKR1 (small lysine rich protein 1, HGNC:43561) is a protein-coding gene on chromosome 7q32.1, encoding Small lysine-rich protein 1 (H3BMG3).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_001195243

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:43561
Approved symbol	SMKR1
Name	small lysine rich protein 1
Location	7q32.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000240204
Ensembl biotype	protein_coding
Entrez	100287482

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000462322, ENST00000488846

RefSeq mRNA: 1 — MANE Select: NM_001195243 NM_001195243

CCDS: CCDS59077

Canonical transcript exons

ENST00000462322 — 2 exons

Exon	Start	End
ENSE00001848602	129502531	129502827
ENSE00001957643	129512247	129512918

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 99.93.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7081 / max 234.5642, expressed in 640 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
81038	1.5779	617
81037	0.1088	38
81039	0.0214	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.93	gold quality
left testis	UBERON:0004533	98.51	gold quality
right testis	UBERON:0004534	98.23	gold quality
oocyte	CL:0000023	98.05	gold quality
secondary oocyte	CL:0000655	96.43	gold quality
testis	UBERON:0000473	95.98	gold quality
adult organism	UBERON:0007023	92.08	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.83	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.40	gold quality
prefrontal cortex	UBERON:0000451	82.81	gold quality
nucleus accumbens	UBERON:0001882	82.74	gold quality
cortical plate	UBERON:0005343	81.33	gold quality
caudate nucleus	UBERON:0001873	80.48	gold quality
right frontal lobe	UBERON:0002810	80.38	gold quality
anterior cingulate cortex	UBERON:0009835	80.36	gold quality
Brodmann (1909) area 9	UBERON:0013540	79.97	gold quality
granulocyte	CL:0000094	79.91	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	79.37	gold quality
putamen	UBERON:0001874	79.25	gold quality
right uterine tube	UBERON:0001302	79.06	gold quality
neocortex	UBERON:0001950	78.57	gold quality
frontal cortex	UBERON:0001870	78.49	gold quality
pituitary gland	UBERON:0000007	78.45	gold quality
adenohypophysis	UBERON:0002196	78.19	gold quality
cerebral cortex	UBERON:0000956	76.35	gold quality
bronchial epithelial cell	CL:0002328	76.33	gold quality
forebrain	UBERON:0001890	76.15	gold quality
amygdala	UBERON:0001876	75.44	gold quality
islet of Langerhans	UBERON:0000006	75.42	gold quality
hypothalamus	UBERON:0001898	75.28	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-38	yes	1751.48
E-GEOD-134144	yes	32.05
E-ANND-3	yes	3.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting SMKR1, 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-4795-3P	100.00	74.62	4024
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-570-3P	99.96	72.41	4910
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-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-8064	99.45	66.92	875
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-520F-5P	99.34	70.40	1632
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-18A-5P	99.29	71.05	806
HSA-MIR-18B-5P	99.29	71.05	806
HSA-MIR-3973	99.20	69.19	1990
HSA-MIR-196A-3P	99.19	67.34	1204
HSA-MIR-8065	99.19	70.38	1289
HSA-MIR-4735-3P	99.14	69.85	777

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	smkr1	ENSDARG00000107526
rattus_norvegicus	Smkr1	ENSRNOG00000070702

Protein

Protein identifiers

Small lysine-rich protein 1 — H3BMG3 (reviewed: H3BMG3)

All UniProt accessions (1): H3BMG3

RefSeq proteins (1): NP_001182172* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037760	SMKR1	Family

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H3BMG3-F1	72.07	0.03

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 38 (showing top): chr7q32, RIGGI_EWING_SARCOMA_PROGENITOR_DN, HOELZEL_NF1_TARGETS_UP, FEV_TARGET_GENES, GLI3_TARGET_GENES, HOXC6_TARGET_GENES, ZSCAN30_TARGET_GENES, MIR182_5P, MIR374A_5P, MIR942_5P, MIR194_5P, GSE11057_EFF_MEM_VS_CENT_MEM_CD4_TCELL_UP, MIR1253, GSE10273_HIGH_IL7_VS_HIGH_IL7_AND_IRF4_IN_IRF4_8_NULL_PRE_BCELL_DN, GSE13306_LAMINA_PROPRIA_VS_SPLEEN_TREG_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

3080 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMKR1	SPATA31A6	Q5VVP1	608
SMKR1	SLFNL1	Q499Z3	602
SMKR1	WDR31	Q8NA23	524
SMKR1	C9orf152	Q5JTZ5	506
SMKR1	Q5T8A5	Q5T8A5	431
SMKR1	RBPMS2	Q6ZRY4	376
SMKR1	ARL4D	P49703	364
SMKR1	CLDN19	Q8N6F1	362
SMKR1	HS6ST3	Q8IZP7	356
SMKR1	YARS1	P54577	350
SMKR1	CNGB1	Q14028	348
SMKR1	BPIFA2	Q96DR5	348
SMKR1	SPINK4	O60575	348
SMKR1	VARS1	P26640	347
SMKR1	FAU	P35544	338

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SMKR1	UBA52	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1): UBA52 (Proximity Label-MS)

ESM2 similar proteins: A0A024R1R8, A1A4Q4, A1CMP1, A2R091, A3N0X3, A5DF06, A6R5Z3, A6S6B0, A6ZWL1, A7F9B8, B0BPQ7, B3GXV7, H3BMG3, O31573, P25886, P47915, Q02642, Q05AK9, Q05AX4, Q06DK3, Q0ULD0, Q13442, Q1DI23, Q1HRV4, Q20588, Q28GR1, Q32KU9, Q32LJ0, Q3E764, Q3UHX2, Q4KLG3, Q4P9Y9, Q4SUE2, Q55F75, Q5ASI4, Q5RCI9, Q60QR6, Q62785, Q66654, Q6C2F3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

579 predictions. Top by Δscore:

Variant	Effect	Δscore
7:129502581:C:T	donor_gain	0.9900
7:129502562:GCC:G	donor_gain	0.9800
7:129502702:G:GT	donor_gain	0.9800
7:129512241:T:A	acceptor_gain	0.9800
7:129512245:A:G	acceptor_gain	0.9800
7:129512231:T:G	acceptor_gain	0.9700
7:129512244:A:AG	acceptor_gain	0.9700
7:129512246:G:GG	acceptor_gain	0.9700
7:129512246:GCCA:G	acceptor_gain	0.9700
7:129502672:G:GG	donor_gain	0.9600
7:129502664:G:T	donor_gain	0.9500
7:129503395:C:CG	donor_gain	0.9500
7:129512233:T:G	acceptor_gain	0.9500
7:129502554:C:G	donor_gain	0.9400
7:129502670:T:TA	donor_gain	0.9400
7:129502671:A:AA	donor_gain	0.9400
7:129512235:T:TA	acceptor_gain	0.9400
7:129503044:T:TA	donor_gain	0.9300
7:129512232:A:AG	acceptor_gain	0.9300
7:129503373:G:GT	donor_gain	0.9200
7:129511576:A:AG	donor_gain	0.9200
7:129512246:GC:G	acceptor_gain	0.9200
7:129512246:GCC:G	acceptor_gain	0.9200
7:129502585:C:T	donor_gain	0.9100
7:129502663:G:GT	donor_gain	0.9100
7:129502664:G:GT	donor_gain	0.9100
7:129511576:A:G	donor_gain	0.9100
7:129502813:C:G	donor_gain	0.9000
7:129503225:G:GT	donor_gain	0.9000
7:129503395:C:G	donor_gain	0.9000

AlphaMissense

422 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:129512394:T:C	F51L	0.961
7:129512396:C:A	F51L	0.961
7:129512396:C:G	F51L	0.961
7:129512325:A:C	S28R	0.931
7:129512327:C:A	S28R	0.931
7:129512327:C:G	S28R	0.931
7:129512376:T:C	C45R	0.931
7:129512378:C:G	C45W	0.905
7:129512395:T:C	F51S	0.900
7:129512365:A:T	N41I	0.894
7:129512359:C:A	A39D	0.880
7:129512345:C:A	N34K	0.875
7:129512345:C:G	N34K	0.875
7:129512391:G:C	G50R	0.870
7:129512356:T:A	I38N	0.856
7:129512335:C:A	A31D	0.855
7:129512358:G:C	A39P	0.848
7:129512347:T:C	L35P	0.847
7:129512392:G:T	G50V	0.844
7:129512366:C:A	N41K	0.835
7:129512366:C:G	N41K	0.835
7:129512361:C:G	H40D	0.824
7:129512380:T:A	L46Q	0.822
7:129512380:T:C	L46P	0.822
7:129512347:T:A	L35H	0.817
7:129512363:C:A	H40Q	0.811
7:129512363:C:G	H40Q	0.811
7:129512368:T:A	V42D	0.811
7:129512391:G:T	G50C	0.806
7:129512320:T:G	I26S	0.801

dbSNP variants (sampled 300 via entrez): RS1000405462 (7:129505448 T>C), RS1000775528 (7:129502523 C>G), RS1000937181 (7:129505069 T>C,G), RS1000999133 (7:129512288 T>C), RS1001439228 (7:129505337 C>G), RS1001469989 (7:129505628 G>A), RS1001637353 (7:129511464 T>A,G), RS1001681682 (7:129506845 G>A), RS1001850511 (7:129502320 C>G), RS1002071190 (7:129502019 C>G), RS1002421723 (7:129508695 C>G), RS1003036960 (7:129513110 G>A), RS1003812708 (7:129504889 T>C), RS1004064776 (7:129510828 A>G), RS1004073139 (7:129504733 T>C)

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

1 associations (top):

Study	Trait	p-value
GCST004639_1	Prudent dietary pattern	7.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	4
mercuric bromide	decreases expression, affects cotreatment	2
Smoke	decreases expression, increases abundance, increases expression	2
Cadmium Chloride	decreases expression, increases expression	2
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
entinostat	increases expression, affects cotreatment	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Cisplatin	decreases expression	1
Estradiol	increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Okadaic Acid	increases expression	1
p-Chloromercuribenzoic Acid	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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