SPATA17

Summary

SPATA17 (spermatogenesis associated 17, HGNC:25184) is a protein-coding gene on chromosome 1q41, encoding Spermatogenesis-associated protein 17 (Q96L03).

Predicted to enable calmodulin binding activity. Predicted to be located in cytoplasm.

Source: NCBI Gene 128153 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 231 total — 1 pathogenic
• MANE Select transcript: NM_138796

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25184
Approved symbol	SPATA17
Name	spermatogenesis associated 17
Location	1q41
Locus type	gene with protein product
Status	Approved
Aliases	IQCH, MOT17, FAP305, CFAP305
Ensembl gene	ENSG00000162814
Ensembl biotype	protein_coding
OMIM	611032
Entrez	128153

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000366933, ENST00000470448, ENST00000471021, ENST00000491809, ENST00000492747, ENST00000905764, ENST00000937952

RefSeq mRNA: 2 — MANE Select: NM_138796 NM_001375655, NM_138796

CCDS: CCDS1519

Canonical transcript exons

ENST00000366933 — 11 exons

Exon	Start	End
ENSE00001909585	217867022	217871696
ENSE00003291707	217648882	217648971
ENSE00003388175	217651097	217651178
ENSE00003489308	217801718	217801850
ENSE00003545552	217741975	217742098
ENSE00003552855	217782174	217782322
ENSE00003580611	217683258	217683361
ENSE00003592896	217774334	217774537
ENSE00003623374	217862774	217862856
ENSE00003660702	217669033	217669083
ENSE00003844303	217631344	217631446

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 97.28.

FANTOM5 (CAGE): breadth broad, TPM avg 2.2504 / max 164.1949, expressed in 813 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
8588	2.0650	749
8587	0.1854	56

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.28	gold quality
bronchial epithelial cell	CL:0002328	96.25	gold quality
left testis	UBERON:0004533	96.16	gold quality
right testis	UBERON:0004534	95.45	gold quality
bronchus	UBERON:0002185	94.33	gold quality
testis	UBERON:0000473	93.61	gold quality
right uterine tube	UBERON:0001302	93.10	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.14	gold quality
corpus epididymis	UBERON:0004359	89.30	gold quality
oviduct epithelium	UBERON:0004804	87.82	gold quality
mucosa of paranasal sinus	UBERON:0005030	86.11	gold quality
caput epididymis	UBERON:0004358	85.73	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.85	gold quality
fallopian tube	UBERON:0003889	81.30	gold quality
adult organism	UBERON:0007023	81.23	gold quality
epithelium of nasopharynx	UBERON:0001951	79.27	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.90	gold quality
cauda epididymis	UBERON:0004360	76.33	gold quality
ventricular zone	UBERON:0003053	72.37	gold quality
buccal mucosa cell	CL:0002336	71.80	silver quality
metanephros cortex	UBERON:0010533	70.74	gold quality
islet of Langerhans	UBERON:0000006	69.69	gold quality
nasal cavity mucosa	UBERON:0001826	69.59	gold quality
adenohypophysis	UBERON:0002196	68.77	gold quality
right lung	UBERON:0002167	68.44	gold quality
adult mammalian kidney	UBERON:0000082	68.12	gold quality
kidney epithelium	UBERON:0004819	67.99	silver quality
nasal cavity epithelium	UBERON:0005384	67.92	gold quality
cortical plate	UBERON:0005343	67.88	gold quality
left lobe of thyroid gland	UBERON:0001120	67.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.49
E-MTAB-9388	yes	7.53

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting SPATA17, 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-8485	100.00	77.57	4731
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-653-5P	99.46	67.35	1300
HSA-MIR-6165	99.44	67.12	1389
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-377-3P	99.37	70.18	1905
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-183-5P	99.31	72.27	1164
HSA-MIR-7974	99.24	65.48	1137

Literature-anchored findings (GeneRIF, showing 2)

• the frequency of the SNP3 allele was significantly elevated in the meiotic arrest group (P < 0.05). This study suggests that SPATA17 may play a critical role in human spermatogenesis, especially in meiosis. (PMID:19483714)
• Elevated production of the SPATA17 protein disturbs the normal development of male germ cells. (PMID:23079716)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	spata17	ENSDARG00000054414
mus_musculus	Spata17	ENSMUSG00000026611
rattus_norvegicus	Spata17	ENSRNOG00000002504
drosophila_melanogaster	CG18063	FBGN0028856
drosophila_melanogaster	CG12448	FBGN0028857
drosophila_melanogaster	CG13544	FBGN0034826
drosophila_melanogaster	CG31735	FBGN0051735

Protein

Protein identifiers

Spermatogenesis-associated protein 17 — Q96L03 (reviewed: Q96L03)

All UniProt accessions (2): Q96L03, R4GN71

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

RefSeq proteins (2): NP_001362584, NP_620151* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000048	IQ_motif_EF-hand-BS	Binding_site
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR051185	ASPM	Family

Pfam: PF00612

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96L03-F1	81.98	0.40

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 172 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_SINGLE_FERTILIZATION, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, HP1SITEFACTOR_Q6, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, AACTTT_UNKNOWN, AML1_01, GOBP_FERTILIZATION, chr15q23, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, LEIN_CHOROID_PLEXUS_MARKERS, GOCC_RIBONUCLEOPROTEIN_GRANULE, SCGGAAGY_ELK1_02

GO Biological Process (0):

GO Molecular Function (2): calmodulin binding (GO:0005516), protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

2415 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA17	SPATA4	Q8NEY3	694
SPATA17	CCDC180	Q9P1Z9	632
SPATA17	RRP15	Q9Y3B9	625
SPATA17	GPATCH2	Q9NW75	621
SPATA17	CFAP92	Q9ULG3	605
SPATA17	SPAG6	O75602	589
SPATA17	DLEC1	Q9Y238	570
SPATA17	KCTD3	Q9Y597	559
SPATA17	DPY30	Q9C005	520
SPATA17	SPATA22	Q8NHS9	518
SPATA17	SPATA7	Q9P0W8	510
SPATA17	GLIPR1L2	Q4G1C9	499
SPATA17	SPATA20	Q8TB22	489
SPATA17	CALM1	P02593	487
SPATA17	CALML6	Q8TD86	487
SPATA17	CALML3	P27482	487

IntAct

18 interactions, top by confidence:

A	B	Type	Score
SPATA17	KDM1B	psi-mi:“MI:0915”(physical association)	0.590
	SPATA17	psi-mi:“MI:0915”(physical association)	0.560
CALR	SPATA17	psi-mi:“MI:0915”(physical association)	0.560
SPATA17	DLST	psi-mi:“MI:0915”(physical association)	0.560
SPATA17	TMEM123	psi-mi:“MI:0915”(physical association)	0.560
SPATA17	NEK7	psi-mi:“MI:0915”(physical association)	0.560
	SPATA17	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (8): KDM1B (Affinity Capture-MS), SPATA17 (Synthetic Lethality), KDM1B (Affinity Capture-MS), SPATA17 (Two-hybrid), SPATA17 (Two-hybrid), CALM1 (Two-hybrid), KDM1B (Affinity Capture-MS), SPATA17 (Positive Genetic)

ESM2 similar proteins: A0A1B0GVH7, A6PVS8, A8DZJ1, A9Q751, D3ZSP7, D4AEC2, Q08AD1, Q08CX2, Q14DL3, Q2T9P0, Q2TA00, Q32KQ1, Q3UZ57, Q3V0J4, Q4G0U5, Q4R7B1, Q4R7Z7, Q5S003, Q5SUV2, Q5T1B0, Q5ZLS8, Q63164, Q66HC0, Q69CM7, Q6AXP3, Q6AYL8, Q6IRN6, Q6NXP0, Q6Q759, Q80X60, Q86WZ0, Q8C1B1, Q8C4J0, Q8C636, Q8CDN1, Q8CDU5, Q8IWF9, Q8N7B9, Q8N7U6, Q8ND61

Diamond homologs: Q4R7Z7, Q96L03, Q9D552

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	173
Likely benign	24
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1199383	Single allele	Pathogenic

SpliceAI

7695 predictions. Top by Δscore:

Variant	Effect	Δscore
15:67261393:GA:G	donor_gain	1.0000
15:67261395:G:GG	donor_gain	1.0000
15:67344061:AG:A	acceptor_gain	1.0000
15:67344062:GG:G	acceptor_gain	1.0000
15:67344170:GCAC:G	donor_gain	1.0000
15:67384934:AG:A	acceptor_gain	1.0000
15:67384935:GG:G	acceptor_gain	1.0000
15:67388825:TTTTA:T	acceptor_loss	1.0000
15:67388826:TTTA:T	acceptor_loss	1.0000
15:67388827:TTAGA:T	acceptor_loss	1.0000
15:67388828:TAG:T	acceptor_loss	1.0000
15:67388829:A:AG	acceptor_gain	1.0000
15:67388829:AGATG:A	acceptor_loss	1.0000
15:67388830:G:GG	acceptor_gain	1.0000
15:67388830:GAT:G	acceptor_gain	1.0000
15:67388968:TTCAA:T	donor_gain	1.0000
15:67388989:GCT:G	donor_gain	1.0000
15:67389002:TCCCT:T	donor_gain	1.0000
15:67389003:CCCTG:C	donor_loss	1.0000
15:67389005:CT:C	donor_gain	1.0000
15:67389006:TGTG:T	donor_loss	1.0000
15:67389007:G:GG	donor_gain	1.0000
15:67389007:GT:G	donor_loss	1.0000
15:67389008:T:A	donor_loss	1.0000
15:67389009:G:GC	donor_loss	1.0000
15:67389010:AGTT:A	donor_loss	1.0000
15:67416929:A:AG	acceptor_gain	1.0000
15:67416930:G:GG	acceptor_gain	1.0000
15:67417049:AAGG:A	donor_loss	1.0000
15:67417052:G:GA	donor_loss	1.0000

AlphaMissense

2357 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:217683270:T:A	W102R	0.986
1:217683270:T:C	W102R	0.986
1:217683274:G:C	R103P	0.978
1:217683289:G:C	R108P	0.969
1:217782180:T:C	F244L	0.967
1:217782182:C:A	F244L	0.967
1:217782182:C:G	F244L	0.967
1:217683263:G:C	Q99H	0.965
1:217683263:G:T	Q99H	0.965
1:217742087:A:C	S170R	0.963
1:217742089:C:A	S170R	0.963
1:217742089:C:G	S170R	0.963
1:217648916:G:C	A35P	0.960
1:217648944:G:C	R44P	0.956
1:217669075:G:C	A95P	0.953
1:217742088:G:T	S170I	0.946
1:217782211:G:C	R254P	0.946
1:217651134:T:A	W66R	0.945
1:217651134:T:C	W66R	0.945
1:217683328:T:C	L121P	0.944
1:217742082:T:C	L168P	0.941
1:217648919:G:C	A36P	0.939
1:217648959:G:C	R49P	0.939
1:217669076:C:A	A95D	0.939
1:217683259:T:C	I98T	0.933
1:217774392:T:C	L193S	0.932
1:217683272:G:C	W102C	0.931
1:217683272:G:T	W102C	0.931
1:217741983:T:C	L135P	0.929
1:217683259:T:G	I98S	0.926

dbSNP variants (sampled 300 via entrez): RS1000012857 (1:217699515 T>A,C), RS1000039363 (1:217651365 T>G), RS1000042834 (1:217737561 G>C), RS1000056563 (1:217789111 A>G), RS1000056813 (1:217640050 T>C), RS1000057951 (1:217704646 G>C), RS1000084934 (1:217820812 AT>A,ATT), RS1000088551 (1:217704936 G>A), RS1000089365 (1:217658215 G>A,T), RS1000095197 (1:217644634 AT>A,ATT), RS1000099738 (1:217861481 A>G), RS1000100180 (1:217779432 C>G), RS1000107857 (1:217739313 C>T), RS1000122533 (1:217770633 T>A), RS1000126268 (1:217677053 A>G)

Disease associations

OMIM: gene MIM:611032 | disease phenotypes: MIM:614816

GenCC curated gene-disease

Mondo (1): Loeys-Dietz syndrome 4 (MONDO:0013897)

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST000880_32	Menarche (age at onset)	2.000000e-06
GCST002829_13	Urate levels in overweight individuals	6.000000e-06
GCST004652_1	Peak velocity of the mitral A-wave	1.000000e-08
GCST007325_196	General risk tolerance (MTAG)	2.000000e-08
GCST008103_41	Bipolar disorder	1.000000e-07
GCST008156_53	Hip circumference adjusted for BMI	3.000000e-06
GCST008514_24	Peginterferon alfa-2a treatment response in chronic hepatitis B infection	3.000000e-06
GCST008916_53	Asthma	1.000000e-19
GCST009764_10	Body mass index	4.000000e-06
GCST009798_20	Asthma	5.000000e-19
GCST009798_50	Asthma	4.000000e-07
GCST009798_54	Asthma	6.000000e-09
GCST009798_80	Asthma	1.000000e-45
GCST012226_365	Waist circumference adjusted for body mass index	1.000000e-08
GCST012490_174	Femur bone mineral density x serum urate levels interaction	3.000000e-08
GCST90000025_851	Appendicular lean mass	2.000000e-16
GCST90013442_25	Keratoconus	2.000000e-26

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0004531	urate measurement
EFO:0008204	left ventricular diastolic function measurement
EFO:0008579	risk-taking behaviour
EFO:0008039	BMI-adjusted hip circumference
EFO:0010103	response to peginterferon alfa-2a
EFO:0004340	body mass index
EFO:0007789	BMI-adjusted waist circumference
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cisplatin	affects cotreatment, decreases expression, affects expression	2
Estradiol	decreases expression, increases reaction	2
Aflatoxin B1	decreases expression, increases methylation	2
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
bisphenol A	decreases expression	1
sulforaphane	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
pentanal	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Decitabine	affects expression	1
Vorinostat	increases expression	1
Air Pollutants	increases expression, increases abundance	1
Amiodarone	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Malathion	decreases expression	1
Melphalan	decreases expression	1
Silicon Dioxide	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	increases expression	1
Permethrin	decreases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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