SPATA31H1

Summary

SPATA31H1 (SPATA31 subfamily H member 1, HGNC:25275) is a protein-coding gene on chromosome 2p23.3, encoding Spermatogenesis-associated protein 31H1 (Q68DN1).

Located in extracellular exosome and nucleus.

Source: NCBI Gene 84226 — RefSeq curated summary.

At a glance

• GWAS associations: 22
• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_032266

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25275
Approved symbol	SPATA31H1
Name	SPATA31 subfamily H member 1
Location	2p23.3
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434G118
Ensembl gene	ENSG00000221843
Ensembl biotype	protein_coding
Entrez	84226

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000447166

RefSeq mRNA: 1 — MANE Select: NM_032266 NM_032266

CCDS: CCDS42666

Canonical transcript exons

ENST00000447166 — 5 exons

Exon	Start	End
ENSE00001619007	27565337	27565415
ENSE00001646972	27566044	27566098
ENSE00001700093	27566735	27582722
ENSE00001708923	27537386	27537570
ENSE00001766240	27566289	27566384

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 91.04.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0217 / max 17.1412, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
19377	0.0175	3
19378	0.0042	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cardiac muscle of right atrium	UBERON:0003379	91.04	gold quality
left ventricle myocardium	UBERON:0006566	90.66	gold quality
sperm	CL:0000019	88.19	gold quality
tibialis anterior	UBERON:0001385	84.88	silver quality
right testis	UBERON:0004534	83.50	gold quality
left testis	UBERON:0004533	82.95	gold quality
testis	UBERON:0000473	80.02	gold quality
myocardium	UBERON:0002349	77.46	gold quality
ileal mucosa	UBERON:0000331	76.21	silver quality
epithelial cell of pancreas	CL:0000083	75.13	gold quality
nasal cavity epithelium	UBERON:0005384	75.05	gold quality
kidney epithelium	UBERON:0004819	72.42	gold quality
deltoid	UBERON:0001476	70.14	gold quality
upper arm skin	UBERON:0004263	69.21	gold quality
cortical plate	UBERON:0005343	68.27	gold quality
stromal cell of endometrium	CL:0002255	65.40	gold quality
quadriceps femoris	UBERON:0001377	65.07	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	64.42	gold quality
vastus lateralis	UBERON:0001379	63.28	gold quality
muscle tissue	UBERON:0002385	60.81	gold quality
germinal epithelium of ovary	UBERON:0001304	60.79	gold quality
ganglionic eminence	UBERON:0004023	60.67	gold quality
biceps brachii	UBERON:0001507	60.63	gold quality
islet of Langerhans	UBERON:0000006	59.77	gold quality
ventricular zone	UBERON:0003053	59.74	silver quality
jejunal mucosa	UBERON:0000399	59.08	gold quality
colonic epithelium	UBERON:0000397	58.50	gold quality
right lobe of liver	UBERON:0001114	58.46	gold quality
bone marrow cell	CL:0002092	57.96	gold quality
skeletal muscle tissue	UBERON:0001134	57.77	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.33
E-MTAB-6058	no	46.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting SPATA31H1, 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-10523-5P	99.91	69.22	2038
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-4451	98.82	68.17	1455
HSA-MIR-4436B-3P	98.25	65.26	1494
HSA-MIR-6735-5P	98.24	65.36	1488
HSA-MIR-7843-5P	98.12	65.26	1421
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-4632-5P	97.82	65.38	1470
HSA-MIR-6879-5P	97.77	65.52	1521
HSA-MIR-1913	97.07	66.20	1417
HSA-MIR-3116	97.07	65.78	1324
HSA-MIR-1237-5P	95.38	62.21	451
HSA-MIR-4488	95.38	62.00	443
HSA-MIR-4697-5P	95.38	61.72	457

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31h1	ENSMUSG00000044581
mus_musculus	Spata31h-ps1	ENSMUSG00000118586
rattus_norvegicus	AABR07063276.1	ENSRNOG00000049398

Protein

Protein identifiers

Spermatogenesis-associated protein 31H1 — Q68DN1 (reviewed: Q68DN1)

All UniProt accessions (1): C9JG08

UniProt curated annotations — full annotation on UniProt →

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

Domain organisation. The P-S-E-R-S-H-H-S repeats give rise to an antiparallel beta-structure.

RefSeq proteins (1): NP_115642* (*=MANE)

Domains & families (InterPro)

UniProt features (67 total): repeat 27, compositionally biased region 20, sequence variant 11, region of interest 6, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q68DN1-F1	34.94	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): CAGCTG_AP4_Q5, AACTTT_UNKNOWN, POU3F2_02, TGGAAA_NFAT_Q4_01, YATGNWAAT_OCT_C, EVI1_02, MIR12123, MIR4443, chr2p23, GSE15659_TREG_VS_TCONV_UP, COMP1_01, OCT1_05, GATAAGR_GATA_C, GSE21546_UNSTIM_VS_ANTI_CD3_STIM_SAP1A_KO_AND_ELK1_KO_DP_THYMOCYTES_DN, OCT1_01

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleus (GO:0005634), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1
extracellular vesicle	1

Protein interactions and networks

STRING

1762 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31H1	CCDC121	Q6ZUS5	768
SPATA31H1	ZNF512	Q96ME7	766
SPATA31H1	GPN1	Q9HCN4	605
SPATA31H1	FNDC4	Q9H6D8	570
SPATA31H1	SLC4A1AP	Q9BWU0	543
SPATA31H1	GCKR	Q14397	540
SPATA31H1	NRBP1	Q9UHY1	448
SPATA31H1	KRTCAP3	Q53RY4	447
SPATA31H1	BUD13	Q9BRD0	443
SPATA31H1	SUPT7L	O94864	399
SPATA31H1	COBLL1	Q53SF7	382
SPATA31H1	IFT172	Q9UG01	372
SPATA31H1	GTF3C2	Q8WUA4	370
SPATA31H1	TRIB1	Q96RU8	366
SPATA31H1	APOA5	Q6Q788	343

IntAct

2 interactions, top by confidence:

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

BioGRID (4): C2orf16 (Affinity Capture-MS), C2orf16 (Affinity Capture-RNA), C2orf16 (Affinity Capture-MS), C2orf16 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GTH6, A0A1B0GUW6, A0A1D5RMD1, A2AQH4, A4FU49, A6NJ88, C4P6S0, D3YU32, E9PAV3, F1QU13, I3L273, J3KML8, P70670, Q32L62, Q3V0E1, Q3V3Q4, Q4R729, Q5H9F3, Q5QJ38, Q5SWP3, Q5U4C1, Q5VWK0, Q5VYM1, Q68DN1, Q6AZ54, Q7TSG5, Q810T2, Q8CH19, Q8K4E0, Q8N3K9, Q8N5Q1, Q8NDH2, Q8TCU4, Q8WNU4, Q8WWL7, Q920R4, Q921B4, Q923B3, Q96JA4, Q96M34

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

924 predictions. Top by Δscore:

Variant	Effect	Δscore
2:27537568:GAG:G	donor_gain	1.0000
2:27537570:GGTA:G	donor_loss	1.0000
2:27566042:A:AG	acceptor_gain	1.0000
2:27566043:G:C	acceptor_loss	1.0000
2:27566043:G:GA	acceptor_gain	1.0000
2:27566096:ATGG:A	donor_loss	1.0000
2:27566097:TG:T	donor_gain	1.0000
2:27566098:GG:G	donor_gain	1.0000
2:27566098:GGT:G	donor_loss	1.0000
2:27566099:G:GC	donor_loss	1.0000
2:27566099:G:GG	donor_gain	1.0000
2:27566100:T:G	donor_loss	1.0000
2:27537571:G:GG	donor_gain	0.9900
2:27537572:T:A	donor_loss	0.9900
2:27565967:A:AG	acceptor_gain	0.9900
2:27565968:A:G	acceptor_gain	0.9900
2:27566043:GA:G	acceptor_gain	0.9900
2:27566043:GATCC:G	acceptor_gain	0.9900
2:27566094:ACATG:A	donor_gain	0.9900
2:27566095:CATG:C	donor_gain	0.9900
2:27566096:ATG:A	donor_gain	0.9900
2:27566101:GAG:G	donor_loss	0.9900
2:27566733:A:AG	acceptor_gain	0.9900
2:27566734:G:GA	acceptor_gain	0.9900
2:27565335:A:AG	acceptor_gain	0.9800
2:27565336:G:GG	acceptor_gain	0.9800
2:27566043:GAT:G	acceptor_gain	0.9800
2:27566043:GATC:G	acceptor_gain	0.9800
2:27566237:A:AG	acceptor_gain	0.9800
2:27566237:ACT:A	acceptor_gain	0.9800

AlphaMissense

35147 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:27580074:T:C	F1168L	0.976
2:27580076:T:A	F1168L	0.976
2:27580076:T:G	F1168L	0.976
2:27580075:T:C	F1168S	0.959
2:27579357:T:C	F929L	0.927
2:27579359:T:A	F929L	0.927
2:27579359:T:G	F929L	0.927
2:27579838:T:C	L1089P	0.923
2:27579504:T:A	W978R	0.919
2:27579504:T:C	W978R	0.919
2:27580617:T:C	F1349L	0.910
2:27580619:C:A	F1349L	0.910
2:27580619:C:G	F1349L	0.910
2:27579506:G:C	W978C	0.896
2:27579506:G:T	W978C	0.896
2:27579862:T:C	L1097P	0.886
2:27580338:T:C	F1256L	0.883
2:27580340:C:A	F1256L	0.883
2:27580340:C:G	F1256L	0.883
2:27579935:C:G	C1121W	0.875
2:27580003:T:C	L1144P	0.871
2:27580009:T:C	I1146T	0.868
2:27580009:T:A	I1146N	0.863
2:27580009:T:G	I1146S	0.863
2:27579865:T:C	L1098S	0.862
2:27578325:T:C	F585L	0.854
2:27578327:T:A	F585L	0.854
2:27578327:T:G	F585L	0.854
2:27579942:T:C	C1124R	0.852
2:27579919:T:C	L1116P	0.849

dbSNP variants (sampled 300 via entrez): RS1000011423 (2:27556023 T>A,C), RS1000096737 (2:27564460 C>G), RS1000156723 (2:27555960 C>A,T), RS1000197723 (2:27541519 G>C,T), RS1000257556 (2:27563342 A>G,T), RS1000328310 (2:27571483 G>A), RS1000330767 (2:27562930 T>G), RS1000435539 (2:27580063 T>C,G), RS1000561360 (2:27541327 T>C), RS1000576604 (2:27548113 C>T), RS1000614979 (2:27554097 G>A), RS1000733246 (2:27547658 G>A,T), RS1000803112 (2:27542621 T>C), RS1000906765 (2:27550002 GATTTTT>G), RS1000952218 (2:27576659 G>T)

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

22 associations (top):

Study	Trait	p-value
GCST000769_3	Calcium levels	7.000000e-06
GCST001006_6	Waist Circumference - Triglycerides (WC-TG)	2.000000e-09
GCST001277_11	Liver enzyme levels (gamma-glutamyl transferase)	4.000000e-13
GCST001841_15	Palmitoleic acid (16:1n-7) levels	1.000000e-09
GCST001905_4	Hypertriglyceridemia	2.000000e-13
GCST003264_205	Post bronchodilator FEV1/FVC ratio	4.000000e-06
GCST003858_1	Oral cavity cancer	4.000000e-08
GCST005308_1	Nonalcoholic fatty liver disease	2.000000e-08
GCST005985_4	Creatinine levels	2.000000e-21
GCST005987_24	Albumin-globulin ratio	4.000000e-10
GCST005999_3	Aspartate aminotransferase levels	1.000000e-12
GCST006014_3	Creatine kinase levels	3.000000e-08
GCST006017_2	Prothrombin time	3.000000e-10
GCST006231_16	Mean arterial pressure	9.000000e-06
GCST007437_11	Triglyceride levels	7.000000e-06
GCST007858_2	Fasting blood glucose adjusted for BMI	4.000000e-09
GCST008103_38	Bipolar disorder	1.000000e-07
GCST008985_2	Triglycerides	7.000000e-12
GCST010276_7	Renal underexcretion gout	5.000000e-07
GCST010660_10	Triglyceride levels	1.000000e-25
GCST011351_3	Aspartate aminotransferase levels	2.000000e-11
GCST90016673_8	Percent liver fat	2.000000e-08

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0004838	calcium measurement
EFO:0000195	metabolic syndrome
EFO:0004530	triglyceride measurement
EFO:0004532	serum gamma-glutamyl transferase measurement
EFO:0004713	FEV/FVC ratio
EFO:0005128	albumin:globulin ratio measurement
EFO:0004736	aspartate aminotransferase measurement
EFO:0004534	creatine kinase measurement
EFO:0008390	prothrombin time measurement
EFO:0006340	mean arterial pressure
EFO:0010821	liver fat measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, affects methylation	2
fluorene-9-bisphenol	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
licochalcone B	decreases expression	1
Cannabidiol	increases expression	1
Endosulfan	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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