STPG3

Summary

STPG3 (sperm-tail PG-rich repeat containing 3, HGNC:37285) is a protein-coding gene on chromosome 9q34.3, encoding Protein STPG3 (Q8N7X2).

Predicted to be active in cytoskeleton.

Source: NCBI Gene 441476 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001004353

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37285
Approved symbol	STPG3
Name	sperm-tail PG-rich repeat containing 3
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40246
Ensembl gene	ENSG00000197768
Ensembl biotype	protein_coding
Entrez	441476

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000388931, ENST00000412566, ENST00000610325, ENST00000611378, ENST00000620243, ENST00000620716, ENST00000622761, ENST00000965010

RefSeq mRNA: 4 — MANE Select: NM_001004353 NM_001004353, NM_001256699, NM_001256700, NM_001256701

CCDS: CCDS48065, CCDS59156, CCDS75940, CCDS75941

Canonical transcript exons

ENST00000412566 — 6 exons

Exon	Start	End
ENSE00001417562	137251738	137251895
ENSE00001420680	137252662	137252965
ENSE00001422331	137252001	137252135
ENSE00001425417	137252437	137252525
ENSE00001680150	137251286	137251396
ENSE00003750661	137253115	137253483

Expression profiles

Bgee: expression breadth ubiquitous, 152 present calls, max score 94.34.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1218 / max 97.4344, expressed in 5 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99684	0.1067	4
99685	0.0112	4
99686	0.0038	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	94.34	gold quality
right testis	UBERON:0004534	93.96	gold quality
testis	UBERON:0000473	90.22	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.26	gold quality
right lobe of liver	UBERON:0001114	83.14	gold quality
right uterine tube	UBERON:0001302	80.71	gold quality
right lobe of thyroid gland	UBERON:0001119	76.51	gold quality
left lobe of thyroid gland	UBERON:0001120	75.00	gold quality
metanephros cortex	UBERON:0010533	74.71	gold quality
mucosa of transverse colon	UBERON:0004991	74.36	gold quality
thyroid gland	UBERON:0002046	73.93	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	69.06	gold quality
pituitary gland	UBERON:0000007	68.99	gold quality
adenohypophysis	UBERON:0002196	68.92	gold quality
body of pancreas	UBERON:0001150	68.88	gold quality
adult mammalian kidney	UBERON:0000082	68.74	gold quality
small intestine Peyer’s patch	UBERON:0003454	68.51	gold quality
cortex of kidney	UBERON:0001225	67.83	gold quality
endocervix	UBERON:0000458	67.45	gold quality
right adrenal gland	UBERON:0001233	66.54	gold quality
small intestine	UBERON:0002108	66.32	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	65.89	gold quality
transverse colon	UBERON:0001157	65.88	gold quality
left adrenal gland cortex	UBERON:0035825	65.64	gold quality
biceps brachii	UBERON:0001507	65.50	gold quality
left adrenal gland	UBERON:0001234	65.19	gold quality
metanephros	UBERON:0000081	64.59	gold quality
adult organism	UBERON:0007023	64.24	gold quality
right adrenal gland cortex	UBERON:0035827	64.23	gold quality
body of stomach	UBERON:0001161	63.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting STPG3, 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-6764-5P	99.75	67.89	2304
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-3154	98.94	66.55	1455
HSA-MIR-4690-3P	97.02	64.72	981
HSA-MIR-5685	97.02	64.34	1004
HSA-MIR-3194-5P	96.80	64.90	1027
HSA-MIR-6856-3P	96.47	66.27	781
HSA-MIR-4264	96.35	64.76	1480
HSA-MIR-6777-5P	88.76	62.64	222
HSA-MIR-4781-5P	88.22	64.40	100

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Stpg3	ENSMUSG00000036770
rattus_norvegicus	Stpg3	ENSRNOG00000010002

Protein

Protein identifiers

Protein STPG3 — Q8N7X2 (reviewed: Q8N7X2)

Alternative names: Sperm-tail PG-rich repeat-containing protein 3

All UniProt accessions (4): A0A087WTN1, A0A087X133, B7ZM74, Q8N7X2

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. Dubious isoform produced through aberrant splice sites.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8N7X2-2	2	yes
Q8N7X2-1	1
Q8N7X2-3	3
Q8N7X2-4	4

RefSeq proteins (4): NP_001004353, NP_001243628, NP_001243629, NP_001243630 (=MANE)

Domains & families (InterPro)

UniProt features (7 total): splice variant 3, chain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7X2-F1	49.70	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): chr9q34, ZNF436_TARGET_GENES, MIR4781_5P, GSE14308_NAIVE_CD4_TCELL_VS_NATURAL_TREG_UP, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_24H_ACT_CD4_TCELL_UP, ZHANG_FH_DEFICIENT_RCC_TUMOR_VS_NORMAL_DN, GSE30083_SP1_VS_SP2_THYMOCYTE_DN, GSE9037_WT_VS_IRAK4_KO_LPS_1H_STIM_BMDM_DN, GSE2405_HEAT_KILLED_VS_LIVE_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_9H_UP, GSE6875_TCONV_VS_FOXP3_KO_TREG_UP, GSE22589_HEALTHY_VS_HIV_INFECTED_DC_DN, GSE24972_WT_VS_IRF8_KO_MARGINAL_ZONE_SPLEEN_BCELL_DN, GSE24972_WT_VS_IRF8_KO_MARGINAL_ZONE_SPLEEN_BCELL_UP, GSE36078_UNTREATED_VS_AD5_INF_MOUSE_LUNG_DC_UP, GSE43863_NAIVE_VS_TH1_EFF_CD4_TCELL_D6_LCMV_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	1

Protein interactions and networks

STRING

74 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STPG3	TEX36	Q5VZQ5	738
STPG3	SLFNL1	Q499Z3	694
STPG3	GLT6D1	Q7Z4J2	671
STPG3	CIMIP2A	Q6J272	620
STPG3	SPPL2C	Q8IUH8	566
STPG3	PRSS58	Q8IYP2	540
STPG3	ZSCAN12	O43309	529
STPG3	CIMAP3	Q8TCI5	448
STPG3	CKAP2L	Q8IYA6	447
STPG3	CDC42SE2	Q9NRR3	431
STPG3	SVIL	O95425	359
STPG3	CAPZA1	P52907	322
STPG3	MEF2A	Q02078	223
STPG3	ABO	P16442	219
STPG3	EPC2	Q52LR7	195

IntAct

3 interactions, top by confidence:

A	B	Type	Score
STPG3	LONP1	psi-mi:“MI:0914”(association)	0.350
STPG3	HAX1	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): LONP1 (Affinity Capture-MS), CAMK1D (Affinity Capture-MS), LONP1 (Affinity Capture-MS), TIMM13 (Affinity Capture-MS), LONP1 (Affinity Capture-MS), TIMM13 (Affinity Capture-MS), CAMK1D (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), RPTOR (Affinity Capture-MS), CLPB (Affinity Capture-MS), HAX1 (Affinity Capture-MS), TUBA1A (Affinity Capture-MS), SARDH (Affinity Capture-MS), MCCC1 (Affinity Capture-MS), C9orf173 (Protein-peptide)

ESM2 similar proteins: A0A1L8HTT5, A1A5R9, A2RSX4, A4IFR8, A5WUY6, A6QPC0, A7YWH3, B0BNE4, E1BNS6, G3X6E2, Q08BC4, Q0P591, Q0VB26, Q14BB9, Q17RG1, Q1XFL1, Q2NKX9, Q2T9Q3, Q2TA11, Q2TBS4, Q3KQ80, Q3SX64, Q3UFT3, Q3ZBR0, Q4QR77, Q4R5Y0, Q4VXA5, Q562E2, Q6J272, Q6ZQR2, Q7T3U0, Q8C8J0, Q8N1D5, Q8N412, Q8N7X2, Q8N801, Q8TCI5, Q8WW14, Q99932, Q9BWG6

Diamond homologs: A2RSX4, Q8N7X2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

779 predictions. Top by Δscore:

Variant	Effect	Δscore
9:137251397:G:GG	donor_gain	1.0000
9:137251888:GGAAC:G	donor_gain	1.0000
9:137251896:G:GG	donor_gain	1.0000
9:137252966:G:GG	donor_gain	1.0000
9:137252971:G:GT	donor_gain	1.0000
9:137251342:G:GT	donor_gain	0.9900
9:137251346:C:T	donor_gain	0.9900
9:137251414:G:GT	donor_gain	0.9900
9:137251414:G:T	donor_gain	0.9900
9:137251422:G:T	donor_gain	0.9900
9:137251435:G:GT	donor_gain	0.9900
9:137251733:TGCA:T	acceptor_loss	0.9900
9:137251734:GCA:G	acceptor_loss	0.9900
9:137251735:CA:C	acceptor_loss	0.9900
9:137251889:G:T	donor_gain	0.9900
9:137251889:GAAC:G	donor_gain	0.9900
9:137251900:G:GG	donor_gain	0.9900
9:137253114:GCCC:G	acceptor_gain	0.9900
9:137251374:C:T	donor_gain	0.9800
9:137251408:A:T	donor_gain	0.9800
9:137251412:G:GT	donor_gain	0.9800
9:137251736:A:AG	acceptor_gain	0.9800
9:137251736:AG:A	acceptor_gain	0.9800
9:137251737:G:GA	acceptor_gain	0.9800
9:137251737:GG:G	acceptor_gain	0.9800
9:137251737:GGCCC:G	acceptor_gain	0.9800
9:137251892:CTAT:C	donor_gain	0.9800
9:137251893:TATG:T	donor_loss	0.9800
9:137251894:ATG:A	donor_loss	0.9800
9:137251898:G:GT	donor_loss	0.9800

AlphaMissense

1993 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:137251317:T:C	F11L	0.982
9:137251319:C:A	F11L	0.982
9:137251319:C:G	F11L	0.982
9:137252490:T:C	F153L	0.972
9:137252492:C:A	F153L	0.972
9:137252492:C:G	F153L	0.972
9:137252508:T:C	F159L	0.971
9:137252510:C:A	F159L	0.971
9:137252510:C:G	F159L	0.971
9:137251329:T:C	F15L	0.970
9:137251331:T:A	F15L	0.970
9:137251331:T:G	F15L	0.970
9:137252920:T:C	F251L	0.953
9:137252922:C:A	F251L	0.953
9:137252922:C:G	F251L	0.953
9:137251355:G:C	W23C	0.922
9:137251355:G:T	W23C	0.922
9:137252469:T:A	W146R	0.920
9:137252469:T:C	W146R	0.920
9:137252459:G:C	W142C	0.916
9:137252459:G:T	W142C	0.916
9:137252662:T:A	W165R	0.910
9:137252662:T:C	W165R	0.910
9:137251318:T:C	F11S	0.908
9:137252713:T:C	F182L	0.908
9:137252715:C:A	F182L	0.908
9:137252715:C:G	F182L	0.908
9:137252664:G:C	W165C	0.907
9:137252664:G:T	W165C	0.907
9:137251353:T:A	W23R	0.899

dbSNP variants (sampled 300 via entrez): RS1000357207 (9:137250582 A>G), RS1000942528 (9:137253731 C>G), RS1000952112 (9:137253537 G>A,C,T), RS1001148781 (9:137249393 T>C), RS1001531715 (9:137253719 A>G,T), RS1002636924 (9:137252437 A>C,G), RS1003259991 (9:137250898 C>A), RS1004307069 (9:137250931 G>A,C,T), RS1004908627 (9:137252035 G>A), RS1005392411 (9:137252246 C>T), RS1005397829 (9:137251066 G>A), RS1007858086 (9:137253434 C>T), RS1008258179 (9:137249511 G>A), RS1008527473 (9:137251745 G>C), RS1008748047 (9:137249730 G>A)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation	2
tetrabromobisphenol A	increases expression	1
benzo(e)pyrene	decreases methylation	1
ferrous chloride	decreases expression	1
Methapyrilene	decreases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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