SPATA31D1

Summary

SPATA31D1 (SPATA31 subfamily D member 1, HGNC:37283) is a protein-coding gene on chromosome 9q21.32, encoding Spermatogenesis-associated protein 31D1 (Q6ZQQ2). May play a role in spermatogenesis.

Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in membrane.

Source: NCBI Gene 389763 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 403 total
• MANE Select transcript: NM_001001670

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37283
Approved symbol	SPATA31D1
Name	SPATA31 subfamily D member 1
Location	9q21.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ46321
Ensembl gene	ENSG00000214929
Ensembl biotype	protein_coding
Entrez	389763

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron

ENST00000344803, ENST00000603921

RefSeq mRNA: 1 — MANE Select: NM_001001670 NM_001001670

CCDS: CCDS47986

Canonical transcript exons

ENST00000344803 — 4 exons

Exon	Start	End
ENSE00001366546	81988772	81989004
ENSE00001371473	81990417	81990486
ENSE00001385751	81990773	81995253
ENSE00001777782	81989778	81989823

Expression profiles

Bgee: expression breadth broad, 17 present calls, max score 92.47.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	92.47	gold quality
upper arm skin	UBERON:0004263	89.06	gold quality
cardiac muscle of right atrium	UBERON:0003379	87.72	gold quality
left ventricle myocardium	UBERON:0006566	86.04	gold quality
epithelium of nasopharynx	UBERON:0001951	84.94	gold quality
cardia of stomach	UBERON:0001162	84.85	gold quality
kidney epithelium	UBERON:0004819	83.75	gold quality
vena cava	UBERON:0004087	82.07	gold quality
lateral nuclear group of thalamus	UBERON:0002736	81.00	gold quality
superficial temporal artery	UBERON:0001614	80.84	gold quality
epithelial cell of pancreas	CL:0000083	80.82	gold quality
vastus lateralis	UBERON:0001379	80.61	gold quality
ventral tegmental area	UBERON:0002691	80.42	gold quality
myocardium	UBERON:0002349	80.28	gold quality
subthalamic nucleus	UBERON:0001906	80.16	gold quality
right testis	UBERON:0004534	80.11	gold quality
dorsal plus ventral thalamus	UBERON:0001897	79.83	gold quality
nasal cavity epithelium	UBERON:0005384	79.43	gold quality
left testis	UBERON:0004533	79.21	gold quality
body of tongue	UBERON:0011876	79.19	gold quality
quadriceps femoris	UBERON:0001377	79.18	gold quality
tongue	UBERON:0001723	79.15	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	79.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.99	gold quality
superior surface of tongue	UBERON:0007371	78.93	gold quality
inferior vagus X ganglion	UBERON:0005363	77.90	gold quality
pharyngeal mucosa	UBERON:0000355	77.89	gold quality
superior vestibular nucleus	UBERON:0007227	77.86	gold quality
pons	UBERON:0000988	77.77	gold quality
lateral globus pallidus	UBERON:0002476	77.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.94

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31f3	ENSMUSG00000050141
rattus_norvegicus		ENSRNOG00000089661

Paralogs (13): SPATA31C2 (ENSG00000177910), SPATA31E1 (ENSG00000177992), SPATA31A6 (ENSG00000185775), SPATA31D3 (ENSG00000186788), SPATA31F3 (ENSG00000187791), SPATA31D4 (ENSG00000189357), SPATA31A1 (ENSG00000204849), SPATA31F1 (ENSG00000205108), SPATA31C1 (ENSG00000230246), (ENSG00000251545), SPATA31A3 (ENSG00000275969), SPATA31A7 (ENSG00000276040), SPATA31A5 (ENSG00000276581)

Protein

Protein identifiers

Spermatogenesis-associated protein 31D1 — Q6ZQQ2 (reviewed: Q6ZQQ2)

Alternative names: Protein FAM75D1

All UniProt accessions (1): Q6ZQQ2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in spermatogenesis.

Subcellular location. Membrane.

Similarity. Belongs to the SPATA31 family.

RefSeq proteins (1): NP_001001670* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain
IPR039509	SPATA31	Domain

Pfam: PF14650, PF15371

UniProt features (11 total): region of interest 5, compositionally biased region 4, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZQQ2-F1	40.19	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, chr9q21, GOBP_SEXUAL_REPRODUCTION, GOBP_REPRODUCTIVE_PROCESS, GOBP_MULTICELLULAR_ORGANISMAL_REPRODUCTIVE_PROCESS, GSE37605_C57BL6_VS_NOD_FOXP3_FUSION_GFP_TREG_UP

GO Biological Process (2): spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
cellular anatomical structure	1

Protein interactions and networks

STRING

448 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31D1	TMEM202	A6NGA9	580
SPATA31D1	SCP2D1	Q9UJQ7	482
SPATA31D1	DDX10	Q13206	476
SPATA31D1	DCAF8L2	P0C7V8	434
SPATA31D1	ZNF738	Q8NE65	419
SPATA31D1	RASEF	Q8IZ41	400
SPATA31D1	NKAIN3	Q8N8D7	395
SPATA31D1	MTNAP1	Q9BSJ5	390
SPATA31D1	GRID1	Q9ULK0	379
SPATA31D1	GRIK3	Q13003	372
SPATA31D1	GRID2	O43424	369
SPATA31D1	ZC2HC1A	Q96GY0	368
SPATA31D1	SPNS3	Q6ZMD2	366
SPATA31D1	GRM7	Q14831	362
SPATA31D1	GRIK1	P39086	360

IntAct

0 interactions, top by confidence:

BioGRID (2): SPATA31D1 (Cross-Linking-MS (XL-MS)), LDHA (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A096LP49, A6NGG8, A6NNH2, B1ASB6, B4DYI2, B6VQA5, C0HKD1, C0HKD2, C0HKD3, D2J0Y4, D6RGX4, E9QAF0, P0C874, P0DKV0, Q149B8, Q3KR64, Q4R736, Q4V8B5, Q5TZJ5, Q5VU36, Q5VVP1, Q5VWK0, Q5VYM1, Q5VYP0, Q63HN1, Q658T7, Q68A65, Q6NS69, Q6NXZ1, Q6PAC4, Q6ZQQ2, Q6ZU69, Q6ZUB0, Q6ZUB1, Q7TSA6, Q80X53, Q86Y26, Q8BHP2, Q8BHW6, Q8C0D9

Diamond homologs: B4DYI2, B6VQA5, E9QAF0, P0C874, P0DKV0, Q5TZJ5, Q5VU36, Q5VVP1, Q5VYP0, Q6ZQQ2, Q6ZUB0, Q6ZUB1, Q8IWB4, A6NFA0, C0HKD1, C0HKD2, C0HKD3, Q32LN6, Q63HN1, Q642A3, Q6ZU69, Q80YD3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	368
Likely benign	31
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

636 predictions. Top by Δscore:

Variant	Effect	Δscore
9:81990758:T:A	acceptor_gain	1.0000
9:81990758:T:TA	acceptor_gain	1.0000
9:81989001:AAAGG:A	donor_loss	0.9900
9:81989002:AAGGT:A	donor_loss	0.9900
9:81989003:AGGTA:A	donor_loss	0.9900
9:81989005:G:C	donor_loss	0.9900
9:81989006:T:A	donor_loss	0.9900
9:81990759:G:A	acceptor_gain	0.9900
9:81990400:T:G	acceptor_gain	0.9800
9:81990764:T:TA	acceptor_gain	0.9800
9:81990908:G:GT	donor_gain	0.9700
9:81988862:GGC:G	donor_gain	0.9600
9:81990771:A:AG	acceptor_gain	0.9600
9:81990772:G:GG	acceptor_gain	0.9600
9:81989776:AGCAT:A	acceptor_gain	0.9500
9:81990312:T:A	acceptor_gain	0.9500
9:81990768:T:A	acceptor_gain	0.9500
9:81990413:TCA:T	acceptor_loss	0.9400
9:81990415:A:AC	acceptor_loss	0.9400
9:81990482:AAAAG:A	donor_loss	0.9400
9:81990483:AAAG:A	donor_loss	0.9400
9:81990484:AAGGT:A	donor_loss	0.9400
9:81990485:AGGTG:A	donor_loss	0.9400
9:81990486:GGTGA:G	donor_loss	0.9400
9:81990487:GTG:G	donor_loss	0.9400
9:81990488:T:A	donor_loss	0.9400
9:81990768:TGCA:T	acceptor_loss	0.9400
9:81990769:GCA:G	acceptor_loss	0.9400
9:81990771:AGCTT:A	acceptor_loss	0.9400
9:81990772:G:A	acceptor_loss	0.9400

AlphaMissense

10332 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:81991980:T:C	F504L	0.972
9:81991982:C:A	F504L	0.972
9:81991982:C:G	F504L	0.972
9:81993198:T:C	F910L	0.937
9:81993200:C:A	F910L	0.937
9:81993200:C:G	F910L	0.937
9:81992499:T:C	F677L	0.928
9:81992501:T:A	F677L	0.928
9:81992501:T:G	F677L	0.928
9:81988915:A:C	S33R	0.904
9:81988917:T:A	S33R	0.904
9:81988917:T:G	S33R	0.904
9:81992004:A:C	S512R	0.903
9:81992006:C:A	S512R	0.903
9:81992006:C:G	S512R	0.903
9:81990843:T:C	C125R	0.901
9:81990858:T:C	C130R	0.892
9:81991986:G:C	G506R	0.891
9:81988924:G:A	G36R	0.887
9:81988924:G:C	G36R	0.887
9:81993150:T:C	F894L	0.877
9:81993152:C:A	F894L	0.877
9:81993152:C:G	F894L	0.877
9:81988837:T:C	F7L	0.876
9:81988839:T:A	F7L	0.876
9:81988839:T:G	F7L	0.876
9:81992064:T:C	F532L	0.870
9:81992066:C:A	F532L	0.870
9:81992066:C:G	F532L	0.870
9:81992568:T:A	W700R	0.868

dbSNP variants (sampled 300 via entrez): RS1000657091 (9:81987927 A>T), RS1000675618 (9:81987549 T>G), RS1000735265 (9:81992608 T>C), RS1003520806 (9:81986193 G>A), RS1003658107 (9:81985825 A>G), RS1003734372 (9:81995631 T>A), RS1004081601 (9:81991256 T>C,G), RS1004320959 (9:81988316 C>G,T), RS1004480271 (9:81992863 G>A,C), RS1004529913 (9:81987248 C>T), RS1004664026 (9:81987056 A>C), RS1005193943 (9:81989873 C>A,G,T), RS1005220728 (9:81991991 C>G,T), RS1005329640 (9:81989533 A>G), RS1005901026 (9:81993754 G>A)

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

7 associations (top):

Study	Trait	p-value
GCST002941_11	Airway imaging phenotypes	7.000000e-07
GCST004521_104	Autism spectrum disorder or schizophrenia	2.000000e-08
GCST004946_105	Schizophrenia	2.000000e-08
GCST006803_104	Schizophrenia	8.000000e-11
GCST007257_11	Broad depression or schizophrenia	2.000000e-09
GCST007576_102	Chronotype	3.000000e-10
GCST009391_2094	Metabolite levels	6.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007627	airway imaging measurement
EFO:0008328	chronotype measurement
EFO:0010373	phosphatidylcholine 32:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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