SPATA19

Summary

SPATA19 (spermatogenesis associated 19, HGNC:30614) is a protein-coding gene on chromosome 11q25, encoding Spermatogenesis-associated protein 19, mitochondrial (Q7Z5L4). Essential for sperm motility and male fertility.

Predicted to be involved in sperm mitochondrion organization. Located in mitochondrion.

Source: NCBI Gene 219938 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 35 total
• MANE Select transcript: NM_174927

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30614
Approved symbol	SPATA19
Name	spermatogenesis associated 19
Location	11q25
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25851, spergen1, SPAS1, CT132
Ensembl gene	ENSG00000166118
Ensembl biotype	protein_coding
OMIM	609805
Entrez	219938

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000299140, ENST00000532889

RefSeq mRNA: 2 — MANE Select: NM_174927 NM_001291992, NM_174927

CCDS: CCDS8493

Canonical transcript exons

ENST00000299140 — 7 exons

Exon	Start	End
ENSE00001099963	133845134	133845190
ENSE00001099969	133844509	133844640
ENSE00001099973	133844246	133844337
ENSE00001099974	133845369	133845513
ENSE00001195074	133842485	133842562
ENSE00001281695	133840631	133840923
ENSE00001281729	133842030	133842105

Expression profiles

Bgee: expression breadth broad, 85 present calls, max score 97.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0642 / max 63.6030, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
123235	0.0642	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	97.98	gold quality
left testis	UBERON:0004533	96.96	gold quality
right testis	UBERON:0004534	96.89	gold quality
sperm	CL:0000019	95.12	gold quality
testis	UBERON:0000473	93.90	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.07	gold quality
adult organism	UBERON:0007023	81.27	gold quality
cartilage tissue	UBERON:0002418	70.55	gold quality
upper leg skin	UBERON:0004262	50.56	silver quality
esophagus mucosa	UBERON:0002469	43.91	gold quality
cardia of stomach	UBERON:0001162	43.82	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
cortical plate	UBERON:0005343	41.33	silver quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
lower esophagus mucosa	UBERON:0035834	41.05	silver quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
middle temporal gyrus	UBERON:0002771	40.87	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting SPATA19, 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-4753-3P	99.90	71.03	3786
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-6738-3P	99.03	67.14	1326
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-4451	98.82	68.17	1455
HSA-MIR-11399	98.71	65.69	869
HSA-MIR-4725-5P	98.67	65.42	628
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-4294	97.86	65.72	1110
HSA-MIR-22-5P	97.67	68.92	1355

Literature-anchored findings (GeneRIF, showing 3)

• The SPATA19 and TEX101 genes may be possible targets for cancer immunotherapy and novel markers for early detection of basal cell carcinoma. (PMID:19886887)
• Of the prostate cancer samples, 10, 10, 23 and 40% showed ODF1, ODF2, LEMD1 and SPATA19 specific bands, respectively, but none of the BPH samples expressed any of these genes. (PMID:20682177)
• Investigated SPATA19 protein expression patterns in a panel of non-malignant samples and primary prostate cancer with or without benign prostatic hyperplasia tissues. SPATA19 was absent in all non-malignant tissues investigated (n=14) except testis and prostate tissues. (PMID:28972294)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata19	ENSMUSG00000031991
rattus_norvegicus	Spata19	ENSRNOG00000031438

Protein

Protein identifiers

Spermatogenesis-associated protein 19, mitochondrial — Q7Z5L4 (reviewed: Q7Z5L4)

Alternative names: Spermatogenic cell-specific gene 1 protein

All UniProt accessions (2): A0A140VKB6, Q7Z5L4

UniProt curated annotations — full annotation on UniProt →

Function. Essential for sperm motility and male fertility. Plays an important role in sperm motility by regulating the organization and function of the mitochondria and is also required for correct sperm midpiece assembly.

Subcellular location. Mitochondrion outer membrane. Mitochondrion. Cell projection. Cilium. Flagellum.

Tissue specificity. Expressed specifically in testis.

RefSeq proteins (2): NP_001278921, NP_777587* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028219	SPATA19	Family

Pfam: PF15212

UniProt features (5 total): modified residue 2, transit peptide 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z5L4-F1	70.74	0.18

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 26, 129

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): GOBP_MALE_GAMETE_GENERATION, GOCC_MITOCHONDRIAL_ENVELOPE, NKX25_01, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, chr11q25, GOCC_MOTILE_CILIUM, GOCC_SPERM_MIDPIECE, GOCC_CILIUM, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, GOCC_ORGANELLE_ENVELOPE, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, GOCC_9PLUS2_MOTILE_CILIUM, GOBP_MITOCHONDRION_ORGANIZATION, MIR4753_3P, MIR4451

GO Biological Process (3): spermatogenesis (GO:0007283), cell differentiation (GO:0030154), sperm mitochondrion organization (GO:0030382)

GO Molecular Function (0):

GO Cellular Component (8): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), sperm flagellum (GO:0036126), sperm midpiece (GO:0097225), cilium (GO:0005929), membrane (GO:0016020), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
mitochondrion organization	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrial membrane	1
organelle outer membrane	1
9+2 motile cilium	1
sperm flagellum	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

802 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA19	OAZ3	Q9UMX2	629
SPATA19	ODF1	Q14990	627
SPATA19	SPATA18	Q8TC71	607
SPATA19	ODF4	Q2M2E3	583
SPATA19	CIMAP1A	Q96PU9	522
SPATA19	TNP2	Q05952	520
SPATA19	SUN5	Q8TC36	509
SPATA19	SPATA3	Q8NHX4	498
SPATA19	SPATA6	Q9NWH7	493
SPATA19	ACRBP	Q8NEB7	476
SPATA19	HMGN5	P82970	464
SPATA19	SPATA45	Q537H7	463
SPATA19	SPEM1	Q8N4L4	462
SPATA19	DKKL1	Q9UK85	451
SPATA19	TSGA10	Q9BZW7	449

IntAct

6 interactions, top by confidence:

A	B	Type	Score
SPATA19	MTHFR	psi-mi:“MI:0914”(association)	0.530
GIGYF1	DYNC1I1	psi-mi:“MI:0914”(association)	0.350
ARID1B	RTCA	psi-mi:“MI:0914”(association)	0.350
TLK2	IGKV1D-13	psi-mi:“MI:0914”(association)	0.350

BioGRID (13): RHEB (Affinity Capture-MS), MFF (Affinity Capture-MS), MTHFR (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), VDAC3 (Affinity Capture-MS), MFF (Affinity Capture-MS), MTHFR (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RHEB (Affinity Capture-MS), VDAC3 (Affinity Capture-MS), SPATA19 (Affinity Capture-MS), SPATA19 (Affinity Capture-MS), SPATA19 (Affinity Capture-MS)

ESM2 similar proteins: A6ZMG4, A6ZR60, B3LLZ8, B6LI37, C5DBV2, C5E1C7, C7GWA2, C8ZEW0, O48767, P34399, P34402, P34518, P35198, P38306, P40063, P40214, P43598, P48437, Q00682, Q02831, Q03564, Q04438, Q06616, Q09599, Q12365, Q15154, Q1T763, Q4R309, Q60JJ0, Q6C3T0, Q6CL13, Q6CQB7, Q6CRT5, Q6CWB2, Q6FWU4, Q6GQM0, Q7Z5L4, Q8AV28, Q8C729, Q8WWF3

Diamond homologs: Q3SZQ3, Q7Z5L4, Q920Q3, Q9DAQ9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1004 predictions. Top by Δscore:

Variant	Effect	Δscore
11:133844480:C:CA	donor_gain	1.0000
11:133842102:TATG:T	acceptor_gain	0.9900
11:133842558:TGTGG:T	acceptor_gain	0.9900
11:133842560:TGG:T	acceptor_gain	0.9900
11:133842563:C:CC	acceptor_gain	0.9900
11:133844240:CCTTA:C	donor_loss	0.9900
11:133844241:CTTA:C	donor_loss	0.9900
11:133844242:TTA:T	donor_loss	0.9900
11:133844243:TACCT:T	donor_loss	0.9900
11:133844244:A:C	donor_loss	0.9900
11:133844336:ACC:A	acceptor_loss	0.9900
11:133844338:C:CG	acceptor_loss	0.9900
11:133844339:T:C	acceptor_loss	0.9900
11:133844637:CTGT:C	acceptor_gain	0.9900
11:133844639:GTCTG:G	acceptor_loss	0.9900
11:133844640:TCTGA:T	acceptor_loss	0.9900
11:133844641:C:CA	acceptor_loss	0.9900
11:133844642:T:C	acceptor_loss	0.9900
11:133845129:CTCA:C	donor_gain	0.9900
11:133845132:A:AC	donor_gain	0.9900
11:133845133:C:CC	donor_gain	0.9900
11:133845353:C:CT	donor_gain	0.9900
11:133845368:CCGAA:C	donor_gain	0.9900
11:133840924:C:CC	acceptor_gain	0.9800
11:133842104:TG:T	acceptor_gain	0.9800
11:133842106:C:CC	acceptor_gain	0.9800
11:133842544:T:C	acceptor_gain	0.9800
11:133844244:ACCT:A	donor_gain	0.9800
11:133844245:CCTC:C	donor_gain	0.9800
11:133844338:C:CC	acceptor_gain	0.9800

AlphaMissense

1102 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:133844250:A:G	W119R	0.997
11:133844250:A:T	W119R	0.997
11:133845431:A:G	W6R	0.997
11:133845431:A:T	W6R	0.997
11:133844248:C:A	W119C	0.995
11:133844248:C:G	W119C	0.995
11:133844258:A:G	F116S	0.992
11:133844257:G:C	F116L	0.987
11:133844257:G:T	F116L	0.987
11:133844259:A:G	F116L	0.987
11:133844251:T:A	R118S	0.986
11:133844251:T:G	R118S	0.986
11:133842547:G:C	F125L	0.985
11:133842547:G:T	F125L	0.985
11:133842549:A:G	F125L	0.985
11:133844252:C:G	R118T	0.985
11:133845145:A:G	W42R	0.985
11:133845145:A:T	W42R	0.985
11:133844267:C:G	R113P	0.983
11:133844249:C:G	W119S	0.979
11:133845141:A:G	L43S	0.979
11:133844264:A:G	I114T	0.978
11:133844264:A:C	I114S	0.976
11:133844272:T:A	R111S	0.975
11:133844272:T:G	R111S	0.975
11:133844253:T:C	R118G	0.974
11:133845409:C:G	R13P	0.974
11:133845442:A:T	I2K	0.973
11:133842506:C:G	R139P	0.972
11:133844252:C:A	R118I	0.972

dbSNP variants (sampled 300 via entrez): RS1000053889 (11:133836361 G>A,C,T), RS1000579548 (11:133835606 T>C), RS1000975124 (11:133842625 G>A), RS1001166481 (11:133841570 G>A), RS1001428472 (11:133842222 C>A), RS1001706698 (11:133836979 T>A), RS1001725373 (11:133845808 A>G), RS1001798749 (11:133845321 G>A), RS1001961268 (11:133840931 G>T), RS1002134141 (11:133847063 C>G,T), RS1002340151 (11:133841135 T>A,C), RS1002806964 (11:133843870 G>A), RS1003000521 (11:133845257 C>A,G,T), RS1003012236 (11:133837857 T>C), RS1003281251 (11:133846350 T>A,C)

Disease associations

OMIM: gene MIM:609805 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST010137_5	Cooked vegetable consumption	6.000000e-09
GCST010172_5	Idiopathic downbeat nystagmus	3.000000e-06

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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation, increases expression	2
CGP 52608	affects binding, increases reaction	1

Clinical trials (associated diseases)

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