SPATA31C2

Summary

SPATA31C2 (SPATA31 subfamily C member 2, HGNC:24508) is a protein-coding gene on chromosome 9q22.1, encoding Spermatogenesis-associated protein 31C2 (B4DYI2). May play a role in spermatogenesis.

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

Source: NCBI Gene 645961 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_001350978

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24508
Approved symbol	SPATA31C2
Name	SPATA31 subfamily C member 2
Location	9q22.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP434M131
Ensembl gene	ENSG00000177910
Ensembl biotype	protein_coding
Entrez	645961

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000324915, ENST00000675441

RefSeq mRNA: 2 — MANE Select: NM_001350978 NM_001166137, NM_001350978

CCDS: CCDS94435, CCDS94436

Canonical transcript exons

ENST00000324915 — 4 exons

Exon	Start	End
ENSE00003324058	88138258	88138475
ENSE00003642713	88132966	88133026
ENSE00003899321	88133594	88133669
ENSE00003903861	88129305	88132710

Expression profiles

Bgee: expression breadth broad, 18 present calls, max score 83.09.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.09	gold quality
right testis	UBERON:0004534	79.40	gold quality
left testis	UBERON:0004533	79.15	gold quality
testis	UBERON:0000473	78.78	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.90	gold quality
colonic epithelium	UBERON:0000397	49.21	gold quality
bone marrow cell	CL:0002092	42.97	gold quality
endometrium	UBERON:0001295	42.50	gold quality
duodenum	UBERON:0002114	41.91	silver quality
Ammon’s horn	UBERON:0001954	41.49	gold quality
bone marrow	UBERON:0002371	41.43	gold quality
mucosa of transverse colon	UBERON:0004991	40.67	silver quality
smooth muscle tissue	UBERON:0001135	40.11	silver quality
vermiform appendix	UBERON:0001154	37.82	gold quality
ganglionic eminence	UBERON:0004023	37.16	gold quality
lymph node	UBERON:0000029	36.79	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
fallopian tube	UBERON:0003889	36.15	gold quality
cerebral cortex	UBERON:0000956	35.95	gold quality
primary visual cortex	UBERON:0002436	35.88	gold quality
sural nerve	UBERON:0015488	35.50	gold quality
right uterine tube	UBERON:0001302	35.40	gold quality
superior frontal gyrus	UBERON:0002661	35.11	gold quality
rectum	UBERON:0001052	34.59	gold quality
Brodmann (1909) area 9	UBERON:0013540	34.29	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
cortex of kidney	UBERON:0001225	33.22	gold quality
temporal lobe	UBERON:0001871	33.09	gold quality
endocervix	UBERON:0000458	32.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting SPATA31C2, 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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-3164	99.02	68.39	1071
HSA-MIR-6820-3P	99.02	68.50	1035
HSA-MIR-758-3P	98.42	68.60	1122
HSA-MIR-376C-3P	97.63	68.88	1263
HSA-MIR-134-5P	97.11	66.52	976
HSA-MIR-3118	97.11	66.58	984
HSA-MIR-939-5P	97.10	65.80	1579
HSA-MIR-3059-3P	96.71	67.08	606
HSA-MIR-1343-5P	96.48	66.06	1506
HSA-MIR-5586-3P	95.51	67.00	805
HSA-MIR-1238-3P	95.27	62.25	552
HSA-MIR-4513	95.04	67.06	727
HSA-MIR-6855-3P	95.04	66.57	725
HSA-MIR-4520-5P	93.54	65.23	140
HSA-MIR-1537-3P	90.51	63.57	105

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31	ENSMUSG00000056223
rattus_norvegicus	Spata31	ENSRNOG00000018202

Paralogs (13): SPATA31E1 (ENSG00000177992), SPATA31A6 (ENSG00000185775), SPATA31D3 (ENSG00000186788), SPATA31F3 (ENSG00000187791), SPATA31D4 (ENSG00000189357), SPATA31A1 (ENSG00000204849), SPATA31F1 (ENSG00000205108), SPATA31D1 (ENSG00000214929), SPATA31C1 (ENSG00000230246), (ENSG00000251545), SPATA31A3 (ENSG00000275969), SPATA31A7 (ENSG00000276040), SPATA31A5 (ENSG00000276581)

Protein

Protein identifiers

Spermatogenesis-associated protein 31C2 — B4DYI2 (reviewed: B4DYI2)

Alternative names: Protein FAM75C2

All UniProt accessions (2): B4DYI2, A0A8I5KWQ5

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 (2): NP_001159609, NP_001337907* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain
IPR039509	SPATA31	Domain

Pfam: PF14650, PF15371

UniProt features (19 total): compositionally biased region 10, region of interest 7, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B4DYI2-F1	40.46	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): GOBP_MALE_GAMETE_GENERATION, chr9q22, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, MIR3059_5P, MIR345_3P, MIR1343_5P, MIR939_5P, MIR6857_5P, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_DN, GSE17974_0H_VS_4H_IN_VITRO_ACT_CD4_TCELL_DN, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_0.5H_ACT_CD4_TCELL_DN, GOBP_SEXUAL_REPRODUCTION, GSE24634_IL4_VS_CTRL_TREATED_NAIVE_CD4_TCELL_DAY7_DN, GOBP_REPRODUCTIVE_PROCESS

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

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

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, C0HKD1, C0HKD2, C0HKD3, Q642A3, A6NFR6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

7374 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000910880 (9:88137988 G>A,C), RS1001263149 (9:88138849 C>A,G), RS1001874619 (9:88131395 C>T), RS1001979859 (9:88137770 G>A), RS1003657405 (9:88135008 G>A), RS1004891327 (9:88133956 A>C), RS1004942179 (9:88133861 G>A,T), RS1005229951 (9:88133333 C>G,T), RS1007787135 (9:88132586 C>T), RS1008235059 (9:88140117 A>C), RS1008288852 (9:88138909 A>G), RS1008568502 (9:88136734 A>G), RS1008584627 (9:88131728 A>G), RS1008624379 (9:88135726 C>A,T), RS1009356133 (9:88138794 T>C)

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

3 associations (top):

Study	Trait	p-value
GCST005024_42	Pursuit maintenance gain	6.000000e-07
GCST006680_1	Nonsyndromic cleft lip with or without cleft palate x sex interaction (2df test)	2.000000e-06
GCST008839_235	Height	1.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008433	pursuit maintenance gain measurement
EFO:0003959	cleft lip
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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