SPATA21

Summary

SPATA21 (spermatogenesis associated 21, HGNC:28026) is a protein-coding gene on chromosome 1p36.13, encoding Spermatogenesis-associated protein 21 (Q7Z572). Involved in the differentiation of haploid spermatids.

Predicted to enable calcium ion binding activity.

Source: NCBI Gene 374955 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_198546

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28026
Approved symbol	SPATA21
Name	spermatogenesis associated 21
Location	1p36.13
Locus type	gene with protein product
Status	Approved
Aliases	spergen-2, spergen2
Ensembl gene	ENSG00000187144
Ensembl biotype	protein_coding
Entrez	374955

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000335496, ENST00000375577, ENST00000466212, ENST00000491418, ENST00000540400, ENST00000612240

RefSeq mRNA: 2 — MANE Select: NM_198546 NM_001353349, NM_198546

CCDS: CCDS172, CCDS85935

Canonical transcript exons

ENST00000335496 — 13 exons

Exon	Start	End
ENSE00001333360	16398643	16398822
ENSE00001333382	16421509	16421557
ENSE00001333383	16421911	16421971
ENSE00001333384	16431338	16431422
ENSE00001333385	16432790	16432924
ENSE00001333388	16437128	16437424
ENSE00003563521	16403968	16404039
ENSE00003583615	16400720	16400892
ENSE00003608567	16409601	16410043
ENSE00003622122	16399344	16399521
ENSE00003652032	16403727	16403844
ENSE00003655553	16409118	16409203
ENSE00003689057	16404967	16405104

Expression profiles

Bgee: expression breadth ubiquitous, 144 present calls, max score 92.59.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	92.59	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	86.96	gold quality
vena cava	UBERON:0004087	85.01	silver quality
tendon of biceps brachii	UBERON:0008188	84.95	silver quality
myocardium	UBERON:0002349	83.42	silver quality
vastus lateralis	UBERON:0001379	80.35	silver quality
sperm	CL:0000019	80.27	gold quality
quadriceps femoris	UBERON:0001377	80.25	silver quality
biceps brachii	UBERON:0001507	79.22	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	78.94	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.55	gold quality
gingival epithelium	UBERON:0001949	78.31	gold quality
superficial temporal artery	UBERON:0001614	77.34	gold quality
pharyngeal mucosa	UBERON:0000355	77.32	silver quality
parotid gland	UBERON:0001831	76.99	gold quality
deltoid	UBERON:0001476	76.55	silver quality
cerebellar vermis	UBERON:0004720	75.55	silver quality
body of tongue	UBERON:0011876	75.53	silver quality
right testis	UBERON:0004534	74.83	gold quality
cardia of stomach	UBERON:0001162	74.65	silver quality
left testis	UBERON:0004533	74.53	gold quality
nipple	UBERON:0002030	74.47	silver quality
nasal cavity epithelium	UBERON:0005384	74.43	gold quality
tongue	UBERON:0001723	74.42	silver quality
trachea	UBERON:0003126	74.36	silver quality
mucosa of sigmoid colon	UBERON:0004993	74.17	silver quality
esophagus squamous epithelium	UBERON:0006920	73.69	gold quality
decidua	UBERON:0002450	73.35	gold quality
testis	UBERON:0000473	73.25	gold quality
pylorus	UBERON:0001166	73.04	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.52
E-ENAD-17	no	123.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

2 targeting SPATA21, 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-6882-3P	98.23	67.01	1119
HSA-MIR-4694-5P	94.62	65.39	532

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-197n1.2	ENSDARG00000042937
mus_musculus	Spata21	ENSMUSG00000045004
rattus_norvegicus	Spata21	ENSRNOG00000009058
drosophila_melanogaster	TpnC47D	FBGN0010423
drosophila_melanogaster	TpnC73F	FBGN0010424
drosophila_melanogaster	TpnC41C	FBGN0013348

Paralogs (5): CAPS (ENSG00000105519), PHF24 (ENSG00000122733), CAPSL (ENSG00000152611), CAPS2 (ENSG00000180881), EFCAB6 (ENSG00000186976)

Protein

Protein identifiers

Spermatogenesis-associated protein 21 — Q7Z572 (reviewed: Q7Z572)

All UniProt accessions (3): Q7Z572, H7C5T0, Q5VXG6

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the differentiation of haploid spermatids.

Isoforms (2)

UniProt ID	Names	Canonical?
Q7Z572-1	1	yes
Q7Z572-2	2

RefSeq proteins (2): NP_001340278, NP_940948* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR043520	SPT21	Family

UniProt features (23 total): compositionally biased region 5, binding site 5, sequence variant 5, region of interest 3, chain 1, domain 1, splice variant 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z572-F1	59.65	0.19

Functional residue map

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

Ligand- & substrate-binding residues (5): 268; 270; 272; 274; 279

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): chr1p36, FIGUEROA_AML_METHYLATION_CLUSTER_3_DN, GSE14769_UNSTIM_VS_20MIN_LPS_BMDM_UP, GSE27786_LIN_NEG_VS_MONO_MAC_DN, GSE27786_BCELL_VS_NEUTROPHIL_DN, GSE28237_FOLLICULAR_VS_LATE_GC_BCELL_DN, GSE7460_CTRL_VS_FOXP3_OVEREXPR_TCONV_DN, GSE5589_LPS_VS_LPS_AND_IL6_STIM_IL10_KO_MACROPHAGE_45MIN_UP, GSE34515_CD16_NEG_VS_POS_MONOCYTE_UP, GOMF_CALCIUM_ION_BINDING

GO Biological Process (0):

GO Molecular Function (2): calcium ion binding (GO:0005509), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
metal ion binding	1
cation binding	1

Protein interactions and networks

STRING

1355 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA21	OR1L3	Q8NH93	571
SPATA21	SPATA3	Q8NHX4	510
SPATA21	SPATA24	Q86W54	503
SPATA21	CLBA1	Q96F83	490
SPATA21	DNAJC4	Q9NNZ3	463
SPATA21	OAZ3	Q9UMX2	427
SPATA21	ADAM32	Q8TC27	374
SPATA21	SPATS2	Q86XZ4	365
SPATA21	SOX17	Q9H6I2	364
SPATA21	SLC35A5	Q9BS91	354
SPATA21	JADE3	Q92613	351
SPATA21	ODF1	Q14990	349
SPATA21	ANKEF1	Q9NU02	349
SPATA21	NDUFAF6	Q330K2	305
SPATA21	SETBP1	Q9Y6X0	303

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CAND1	GTPBP10	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): SPATA21 (Affinity Capture-RNA), SPATA21 (Affinity Capture-MS)

ESM2 similar proteins: A2ADZ8, A6NNH2, D2J0Y4, D3YU32, P0C2Y1, Q0VET5, Q12802, Q14676, Q149B8, Q283Q6, Q2TBI7, Q3KR64, Q3U0P1, Q4KMZ1, Q4R736, Q5QJ38, Q5R5G4, Q5T1N1, Q5TM68, Q5VWK0, Q5VYM1, Q5ZK13, Q68A65, Q6AZ54, Q6NXZ1, Q6PG16, Q6PIX9, Q7YR40, Q7Z572, Q86Y26, Q8BHP2, Q8BHW6, Q8C0D9, Q8C5V8, Q8C9M2, Q8CGM2, Q8N5Q1, Q8NCD3, Q8WP21, Q924C5

Diamond homologs: O74435, P02597, P04464, P05419, P13868, P15845, P25071, P27161, P27163, Q0IQB6, Q0IUU4, Q2T9P0, Q40302, Q41420, Q4R736, Q66HC0, Q68A65, Q7Z572, Q80X60, Q84MN0, Q8BHW6, Q8K4K1, Q8N7B9, Q9LE22, A3E3H0, A3E4D8, A3E4F9, A4UHC0, A8I1Q0, O02367, O16305, O82018, O82659, O96081, O97341, P02591, P02598, P02599, P04352, P07463

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	8
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2932 predictions. Top by Δscore:

Variant	Effect	Δscore
1:16393478:GACAG:G	donor_gain	1.0000
1:16393479:ACAG:A	donor_gain	1.0000
1:16393479:ACAGG:A	donor_loss	1.0000
1:16393480:CAGG:C	donor_loss	1.0000
1:16393481:AG:A	donor_gain	1.0000
1:16393482:GG:G	donor_gain	1.0000
1:16393482:GGTG:G	donor_loss	1.0000
1:16393483:G:GA	donor_loss	1.0000
1:16393483:G:GG	donor_gain	1.0000
1:16393484:T:A	donor_loss	1.0000
1:16400716:TCACC:T	donor_loss	1.0000
1:16400717:CAC:C	donor_loss	1.0000
1:16400718:A:AC	donor_gain	1.0000
1:16400719:C:CC	donor_gain	1.0000
1:16400893:C:CC	acceptor_gain	1.0000
1:16403725:A:AC	donor_gain	1.0000
1:16403726:C:CC	donor_gain	1.0000
1:16403736:T:TA	donor_gain	1.0000
1:16404962:CTCA:C	donor_loss	1.0000
1:16404963:TCACC:T	donor_loss	1.0000
1:16404965:A:AC	donor_gain	1.0000
1:16404965:AC:A	donor_gain	1.0000
1:16404966:C:CA	donor_gain	1.0000
1:16404966:CC:C	donor_gain	1.0000
1:16404966:CCA:C	donor_gain	1.0000
1:16405100:GAAGG:G	acceptor_gain	1.0000
1:16405101:AAGG:A	acceptor_gain	1.0000
1:16405102:AGG:A	acceptor_gain	1.0000
1:16405103:GG:G	acceptor_gain	1.0000
1:16405105:C:CC	acceptor_gain	1.0000

AlphaMissense

3052 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:16404011:G:C	F280L	0.989
1:16404011:G:T	F280L	0.989
1:16404013:A:G	F280L	0.989
1:16404012:A:G	F280S	0.984
1:16405088:A:C	F230L	0.984
1:16405088:A:T	F230L	0.984
1:16405090:A:G	F230L	0.984
1:16403792:A:C	F312L	0.982
1:16403792:A:T	F312L	0.982
1:16403794:A:G	F312L	0.982
1:16405101:A:G	F226S	0.979
1:16405100:G:C	F226L	0.975
1:16405100:G:T	F226L	0.975
1:16405102:A:G	F226L	0.975
1:16403981:G:C	F290L	0.973
1:16403981:G:T	F290L	0.973
1:16403983:A:G	F290L	0.973
1:16404020:G:C	F277L	0.972
1:16404020:G:T	F277L	0.972
1:16404022:A:G	F277L	0.972
1:16403757:A:G	L324S	0.971
1:16405047:A:G	L244P	0.968
1:16400888:A:C	Y336D	0.966
1:16409933:G:C	F85L	0.966
1:16409933:G:T	F85L	0.966
1:16409935:A:G	F85L	0.966
1:16403994:T:A	D286V	0.963
1:16405093:A:C	Y229D	0.960
1:16403733:A:C	I332S	0.958
1:16403793:A:G	F312S	0.956

dbSNP variants (sampled 300 via entrez): RS1000015713 (1:16411034 A>G), RS1000107244 (1:16409282 C>G,T), RS1000171612 (1:16408175 G>T), RS1000178275 (1:16425962 T>C,G), RS1000244200 (1:16422957 G>T), RS1000315739 (1:16422482 A>G), RS1000338045 (1:16432248 A>G), RS1000392928 (1:16438562 T>C), RS1000560881 (1:16409122 C>G,T), RS1000573177 (1:16435409 C>T), RS1000660260 (1:16402179 C>T), RS1000733415 (1:16401966 T>G), RS1000876134 (1:16415156 G>A,C), RS1000920820 (1:16407025 G>A), RS1001078230 (1:16433668 C>A,G)

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

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	2
aristolochic acid I	increases expression	1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acid	affects methylation, increases abundance	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	decreases methylation	1
Cannabinoids	increases abundance, affects methylation	1
Methapyrilene	decreases methylation	1
Urethane	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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