SPACDR

Summary

SPACDR (sperm acrosome developmental regulator, HGNC:22135) is a protein-coding gene on chromosome 7q22.1, encoding Sperm acrosome developmental regulator (Q8IZ16). May play a role in acrosome formation and nucleus shaping during spermiogenesis.

Involved in spermatid development. Located in acrosomal vesicle.

Source: NCBI Gene 402573 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001004323

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22135
Approved symbol	SPACDR
Name	sperm acrosome developmental regulator
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Aliases	IMAGE:4839025
Ensembl gene	ENSG00000185955
Ensembl biotype	protein_coding
OMIM	619782
Entrez	402573

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000332375, ENST00000418952

RefSeq mRNA: 1 — MANE Select: NM_001004323 NM_001004323

CCDS: CCDS47661

Canonical transcript exons

ENST00000332375 — 3 exons

Exon	Start	End
ENSE00001321685	100463363	100463686
ENSE00001653812	100463963	100464260
ENSE00001752351	100456620	100456985

Expression profiles

Bgee: expression breadth ubiquitous, 159 present calls, max score 94.42.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1358 / max 168.7058, expressed in 4 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85200	0.1234	3
85199	0.0108	4
85198	0.0017	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	94.42	gold quality
right testis	UBERON:0004534	94.08	gold quality
testis	UBERON:0000473	91.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.73	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.53	gold quality
sperm	CL:0000019	75.71	silver quality
spinal cord	UBERON:0002240	75.55	gold quality
tibial nerve	UBERON:0001323	74.87	gold quality
caudate nucleus	UBERON:0001873	74.72	gold quality
lower esophagus mucosa	UBERON:0035834	74.65	gold quality
pancreatic ductal cell	CL:0002079	74.56	silver quality
amygdala	UBERON:0001876	74.09	gold quality
hypothalamus	UBERON:0001898	73.72	gold quality
adult organism	UBERON:0007023	73.69	gold quality
putamen	UBERON:0001874	73.28	gold quality
granulocyte	CL:0000094	72.25	gold quality
stromal cell of endometrium	CL:0002255	71.46	gold quality
nucleus accumbens	UBERON:0001882	71.44	gold quality
substantia nigra	UBERON:0002038	71.43	gold quality
blood	UBERON:0000178	70.85	gold quality
right frontal lobe	UBERON:0002810	70.51	gold quality
anterior cingulate cortex	UBERON:0009835	70.46	gold quality
Brodmann (1909) area 9	UBERON:0013540	70.22	gold quality
Ammon’s horn	UBERON:0001954	69.99	gold quality
cerebellar hemisphere	UBERON:0002245	69.95	gold quality
cerebellar cortex	UBERON:0002129	69.86	gold quality
right hemisphere of cerebellum	UBERON:0014890	69.83	gold quality
cerebellum	UBERON:0002037	68.99	gold quality
midbrain	UBERON:0001891	68.19	gold quality
forebrain	UBERON:0001890	67.94	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting SPACDR, 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-185-3P	99.95	67.01	1743
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-6864-5P	98.38	66.59	1079
HSA-MIR-3179	98.22	65.90	1445

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tsc22d4	ENSMUSG00000029723

Protein

Protein identifiers

Sperm acrosome developmental regulator — Q8IZ16 (reviewed: Q8IZ16)

All UniProt accessions (2): H7C3K1, Q8IZ16

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in acrosome formation and nucleus shaping during spermiogenesis.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Acrosome.

Tissue specificity. Expressed in sperm (at protein level).

Disease relevance. A variant causing a frameshift predicted to result in a premature termination codon has been found in a patient with globozoospermia.

RefSeq proteins (1): NP_001004323* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031534	SPACDR	Family

Pfam: PF15775

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IZ16-F1	61.81	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): GOCC_SECRETORY_GRANULE, GOBP_MALE_GAMETE_GENERATION, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOCC_SECRETORY_VESICLE, GOCC_ACROSOMAL_VESICLE, ZNF512_TARGET_GENES, MIR3145_3P, MIR4802_3P, MIR185_3P, chr7q22, DESCARTES_FETAL_MUSCLE_MEGAKARYOCYTES, GOBP_SEXUAL_REPRODUCTION, HE_LIM_SUN_FETAL_LUNG_C3_MID_CAP_CELL, GOBP_REPRODUCTIVE_PROCESS

GO Biological Process (3): spermatid development (GO:0007286), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (0):

GO Cellular Component (3): acrosomal vesicle (GO:0001669), nucleus (GO:0005634), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
germ cell development	1
spermatid differentiation	1
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
secretory granule	1
intracellular membrane-bounded organelle	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

270 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPACDR	SPATA16	Q9BXB7	679
SPACDR	CATSPERT	Q53TS8	678
SPACDR	ZPBP	Q9BS86	647
SPACDR	DPY19L2	Q6NUT2	635
SPACDR	PPP1R35	Q8TAP8	571
SPACDR	DNAH17	Q9UFH2	530
SPACDR	CCDC62	Q6P9F0	518
SPACDR	PILRB	Q9UKJ0	473
SPACDR	TSC22D4	Q9Y3Q8	448
SPACDR	PILRA	Q9UKJ1	447
SPACDR	ZCWPW1	Q9H0M4	447
SPACDR	SPACA1	Q9HBV2	438
SPACDR	CFAP276	Q5T5A4	418
SPACDR	ROPN1	Q9HAT0	408
SPACDR	FSIP2	Q5CZC0	405

IntAct

0 interactions, top by confidence:

BioGRID (1): C7orf61 (Synthetic Lethality)

ESM2 similar proteins: A0A1L8I316, A6NCN8, A6NFA0, A6NFR6, A6NJB7, A6NL46, A6QP24, A6QQS3, A8MUI8, A8MX80, B2RW88, B7ZNG4, D3ZUE1, Q05860, Q0P670, Q0VD86, Q12815, Q15583, Q1LZE2, Q1RN00, Q2HR82, Q32LI3, Q32LN6, Q3B8N5, Q5BMD4, Q5DU28, Q5IS58, Q5NCP0, Q5SSG4, Q5SSZ7, Q66H53, Q68DA7, Q68DV7, Q6PE65, Q7TPN9, Q80U22, Q80VY2, Q80YD3, Q8BII1, Q8IZ16

Diamond homologs: Q2T9X5, Q6AY52, Q8IZ16

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

283 predictions. Top by Δscore:

Variant	Effect	Δscore
7:100456983:TGA:T	acceptor_gain	1.0000
7:100456986:C:CC	acceptor_gain	1.0000
7:100456981:GATGA:G	acceptor_gain	0.9900
7:100456982:ATGA:A	acceptor_gain	0.9900
7:100456984:GA:G	acceptor_gain	0.9900
7:100456984:GAC:G	acceptor_loss	0.9900
7:100456985:AC:A	acceptor_loss	0.9900
7:100456986:C:G	acceptor_loss	0.9900
7:100456988:G:C	acceptor_gain	0.9900
7:100463357:GCTGA:G	donor_loss	0.9900
7:100463358:CTGA:C	donor_loss	0.9900
7:100463359:TGACC:T	donor_loss	0.9900
7:100463360:GACC:G	donor_loss	0.9900
7:100463361:AC:A	donor_loss	0.9900
7:100463362:C:CG	donor_loss	0.9900
7:100463365:T:TA	donor_gain	0.9900
7:100463684:AACC:A	acceptor_loss	0.9900
7:100463688:T:G	acceptor_loss	0.9900
7:100463695:C:CT	acceptor_gain	0.9900
7:100463696:A:T	acceptor_gain	0.9900
7:100456988:G:GC	acceptor_gain	0.9800
7:100463695:C:T	acceptor_gain	0.9800
7:100463700:C:CT	acceptor_gain	0.9800
7:100463682:AAAAC:A	acceptor_gain	0.9700
7:100463687:C:CC	acceptor_gain	0.9700
7:100463702:C:CT	acceptor_gain	0.9700
7:100456985:ACTGT:A	acceptor_gain	0.9600
7:100456986:CTGT:C	acceptor_gain	0.9600
7:100463685:AC:A	acceptor_gain	0.9600
7:100463686:CC:C	acceptor_gain	0.9600

AlphaMissense

1313 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:100463418:A:T	V111D	0.890
7:100464005:G:C	F7L	0.879
7:100464005:G:T	F7L	0.879
7:100464007:A:G	F7L	0.879
7:100463405:C:A	M115I	0.856
7:100463405:C:G	M115I	0.856
7:100463405:C:T	M115I	0.856
7:100463983:A:G	W15R	0.848
7:100463983:A:T	W15R	0.848
7:100456898:A:C	Y159D	0.842
7:100456879:A:T	V165D	0.837
7:100463381:C:A	W123C	0.837
7:100463381:C:G	W123C	0.837
7:100456876:C:G	R166P	0.821
7:100456761:A:C	S204R	0.807
7:100456761:A:T	S204R	0.807
7:100456763:T:G	S204R	0.807
7:100463394:A:G	L119P	0.807
7:100463366:C:A	W128C	0.800
7:100463366:C:G	W128C	0.800
7:100463363:C:A	K129N	0.793
7:100463363:C:G	K129N	0.793
7:100463430:G:T	A107D	0.792
7:100463994:A:T	V11D	0.784
7:100456883:C:G	A164P	0.773
7:100456867:A:G	L169P	0.770
7:100463422:A:G	S110P	0.767
7:100463385:C:T	G122D	0.760
7:100463397:G:T	A118D	0.756
7:100456894:A:G	L160P	0.755

dbSNP variants (sampled 300 via entrez): RS1000139196 (7:100464315 A>T), RS1000344392 (7:100462850 C>T), RS1000621242 (7:100456306 C>G), RS1001127552 (7:100465982 A>T), RS1001211671 (7:100458240 A>G), RS1001442153 (7:100460599 AAGAG>A,AAG,AAGAGAG,AAGAGAGAG), RS1001728055 (7:100458551 T>C), RS1001746269 (7:100460874 C>A), RS1001763906 (7:100465685 G>A), RS1002345628 (7:100459346 A>G), RS1003327514 (7:100461614 C>T), RS1004340599 (7:100463477 C>T), RS1005228210 (7:100464893 A>G), RS1005346371 (7:100465199 G>A,C), RS1005362866 (7:100465624 C>G)

Disease associations

OMIM: gene MIM:619782 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST006979_142	Heel bone mineral density	1.000000e-12
GCST010702_48	Subcortical volume (MOSTest)	6.000000e-10
GCST010703_289	Brain morphology (MOSTest)	6.000000e-15
GCST90002401_461	Platelet distribution width	1.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density
EFO:0004346	neuroimaging measurement
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
abrine	decreases expression	1
licochalcone B	increases expression	1
jinfukang	decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Arsenic	affects methylation	1
Copper	affects binding, decreases expression	1
Disulfiram	affects binding, decreases expression	1
Estradiol	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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