SPATA31F1

Summary

SPATA31F1 (SPATA31 subfamily F member 1, HGNC:41911) is a protein-coding gene on chromosome 9p13.3, encoding Protein SPATA31F1 (Q6ZU69).

Located in nucleus.

Source: NCBI Gene 259308 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 5 total — 1 pathogenic
• MANE Select transcript: NM_001141917

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41911
Approved symbol	SPATA31F1
Name	SPATA31 subfamily F member 1
Location	9p13.3
Locus type	gene with protein product
Status	Approved
Aliases	C9orf144B
Ensembl gene	ENSG00000205108
Ensembl biotype	protein_coding
Entrez	259308

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000378788

RefSeq mRNA: 1 — MANE Select: NM_001141917 NM_001141917

CCDS: CCDS55305

Canonical transcript exons

ENST00000378788 — 4 exons

Exon	Start	End
ENSE00001540141	34728022	34728082
ENSE00001540142	34728609	34728654
ENSE00001540143	34729284	34729488
ENSE00001625189	34723053	34726988

Expression profiles

Bgee: expression breadth broad, 25 present calls, max score 83.81.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0306 / max 23.8367, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
100544	0.0175	3
100545	0.0131	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	83.81	gold quality
right testis	UBERON:0004534	83.35	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.29	gold quality
testis	UBERON:0000473	81.11	gold quality
adult organism	UBERON:0007023	66.74	gold quality
pancreatic ductal cell	CL:0002079	54.63	silver quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
epithelial cell of pancreas	CL:0000083	54.00	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
tibialis anterior	UBERON:0001385	51.82	silver quality
myocardium	UBERON:0002349	50.25	gold quality
deltoid	UBERON:0001476	49.96	gold quality
sural nerve	UBERON:0015488	48.38	gold quality
upper leg skin	UBERON:0004262	47.17	silver quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
quadriceps femoris	UBERON:0001377	46.70	gold quality
ileal mucosa	UBERON:0000331	46.51	silver quality
vastus lateralis	UBERON:0001379	45.60	gold quality
colonic epithelium	UBERON:0000397	45.52	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	44.00	silver quality
cortical plate	UBERON:0005343	43.78	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
descending thoracic aorta	UBERON:0002345	42.82	gold quality
skeletal muscle tissue	UBERON:0001134	42.78	gold quality
amniotic fluid	UBERON:0000173	42.74	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting SPATA31F1, 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-3688-3P	99.97	72.02	2834
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-760	98.81	66.65	1392
HSA-MIR-939-5P	97.10	65.80	1579
HSA-MIR-1343-5P	96.48	66.06	1506

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31f1a	ENSMUSG00000078721
mus_musculus	Spata31f1e	ENSMUSG00000078722
mus_musculus	Spata31f1d	ENSMUSG00000078746
mus_musculus	Spata31f1c	ENSMUSG00000093996
mus_musculus	Spata31f1b	ENSMUSG00000094066
rattus_norvegicus	Spata31f1	ENSRNOG00000042596

Paralogs (13): SPATA31C2 (ENSG00000177910), SPATA31E1 (ENSG00000177992), SPATA31A6 (ENSG00000185775), SPATA31D3 (ENSG00000186788), SPATA31F3 (ENSG00000187791), SPATA31D4 (ENSG00000189357), SPATA31A1 (ENSG00000204849), SPATA31D1 (ENSG00000214929), SPATA31C1 (ENSG00000230246), (ENSG00000251545), SPATA31A3 (ENSG00000275969), SPATA31A7 (ENSG00000276040), SPATA31A5 (ENSG00000276581)

Protein

Protein identifiers

Protein SPATA31F1 — Q6ZU69 (reviewed: Q6ZU69)

Alternative names: Protein FAM205A

All UniProt accessions (1): Q6ZU69

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SPATA31 family.

RefSeq proteins (1): NP_001135389* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain
IPR039509	SPATA31	Domain

Pfam: PF14650, PF15371

UniProt features (23 total): sequence conflict 11, compositionally biased region 5, region of interest 5, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZU69-F1	42.69	0.03

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): FOSTER_TOLERANT_MACROPHAGE_DN, chr9p13, MIR539_5P, GSE13229_IMM_VS_INTMATURE_NKCELL_UP, GSE14308_TH17_VS_NAIVE_CD4_TCELL_DN, GSE14308_NAIVE_CD4_TCELL_VS_INDUCED_TREG_UP, GSE14308_NAIVE_CD4_TCELL_VS_NATURAL_TREG_UP, GSE29615_CTRL_VS_DAY7_LAIV_FLU_VACCINE_PBMC_DN, GSE5099_MONOCYTE_VS_CLASSICAL_M1_MACROPHAGE_UP, GSE19772_CTRL_VS_HCMV_INF_MONOCYTES_DN, GSE22229_UNTREATED_VS_IMMUNOSUPP_THERAPY_RENAL_TRANSPLANT_PATIENT_PBMC_UP, GSE21379_TFH_VS_NON_TFH_SAP_KO_CD4_TCELL_DN, GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_UP, GSE25088_CTRL_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DN, GSE40666_STAT1_KO_VS_STAT4_KO_CD8_TCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

218 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31F1	TMEM89	A2RUT3	583
SPATA31F1	SPEM3	A0A1B0GUW6	583
SPATA31F1	IQCF5	A8MTL0	581
SPATA31F1	GARIN3	Q8TC56	539
SPATA31F1	FAM219A	Q8IW50	528
SPATA31F1	PROCA1	Q8NCQ7	525
SPATA31F1	TEX38	Q6PEX7	507
SPATA31F1	PRR30	Q53SZ7	505
SPATA31F1	FSIP2	Q5CZC0	495
SPATA31F1	SPATA3	Q8NHX4	483
SPATA31F1	OR52E4	Q8NGH9	480
SPATA31F1	CIMIP2A	Q6J272	472
SPATA31F1	NT5C1B	Q96P26	447
SPATA31F1	RPP25L	Q8N5L8	434
SPATA31F1	ARID3C	A6NKF2	433

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CRK	SPATA31F1	psi-mi:“MI:0407”(direct interaction)	0.440
P		psi-mi:“MI:0914”(association)	0.350

BioGRID (1): FAM205A (Protein-peptide)

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: A6NFA0, C0HKD1, C0HKD2, C0HKD3, Q32LN6, Q642A3, Q6ZU69, Q80YD3, Q63HN1, Q6ZQQ2, P0C874, Q6ZUB0

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	1
Likely pathogenic	0
Uncertain significance	2
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1070621	NC_000009.11:g.(?34459004)(36276941_?)del	Pathogenic

SpliceAI

534 predictions. Top by Δscore:

Variant	Effect	Δscore
9:34728017:ATCAC:A	donor_loss	1.0000
9:34728018:TCACC:T	donor_loss	1.0000
9:34728019:CACCT:C	donor_loss	1.0000
9:34728020:A:T	donor_loss	1.0000
9:34726985:CTGG:C	acceptor_gain	0.9900
9:34728079:CTAG:C	acceptor_gain	0.9900
9:34728083:C:CC	acceptor_gain	0.9900
9:34726986:TGG:T	acceptor_gain	0.9800
9:34726989:C:CC	acceptor_gain	0.9800
9:34728016:GATCA:G	donor_loss	0.9800
9:34729245:T:C	donor_gain	0.9800
9:34728080:TAG:T	acceptor_gain	0.9700
9:34728081:AG:A	acceptor_gain	0.9700
9:34726987:GG:G	acceptor_gain	0.9600
9:34728077:TCCTA:T	acceptor_gain	0.9600
9:34728091:C:CT	acceptor_gain	0.9500
9:34729233:ATAGG:A	donor_gain	0.9500
9:34725485:C:CT	acceptor_gain	0.9400
9:34729348:A:C	donor_gain	0.9400
9:34728806:CCTTT:C	donor_gain	0.9300
9:34729340:G:A	donor_gain	0.9300
9:34727400:T:TA	donor_gain	0.9200
9:34728790:T:TA	donor_gain	0.9000
9:34729315:A:AC	donor_gain	0.9000
9:34728656:T:C	acceptor_gain	0.8900
9:34726876:T:A	donor_gain	0.8800
9:34729233:A:AC	donor_gain	0.8800
9:34729399:T:TA	donor_gain	0.8800
9:34729400:C:A	donor_gain	0.8800
9:34729025:T:TA	donor_gain	0.8700

AlphaMissense

8727 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:34726318:A:G	W308R	0.954
9:34726318:A:T	W308R	0.954
9:34725941:G:C	F433L	0.941
9:34725941:G:T	F433L	0.941
9:34725943:A:G	F433L	0.941
9:34726316:C:A	W308C	0.930
9:34726316:C:G	W308C	0.930
9:34726325:G:C	F305L	0.916
9:34726325:G:T	F305L	0.916
9:34726327:A:G	F305L	0.916
9:34724888:G:C	F784L	0.914
9:34724888:G:T	F784L	0.914
9:34724890:A:G	F784L	0.914
9:34724561:G:C	F893L	0.865
9:34724561:G:T	F893L	0.865
9:34724563:A:G	F893L	0.865
9:34726981:A:G	W87R	0.862
9:34726981:A:T	W87R	0.862
9:34726317:C:G	W308S	0.859
9:34725917:A:C	S441R	0.855
9:34725917:A:T	S441R	0.855
9:34725919:T:G	S441R	0.855
9:34726308:G:T	P311Q	0.853
9:34726943:A:C	C99W	0.842
9:34726291:A:G	S317P	0.837
9:34724900:C:A	K780N	0.836
9:34724900:C:G	K780N	0.836
9:34726111:A:G	W377R	0.836
9:34726111:A:T	W377R	0.836
9:34726945:A:G	C99R	0.836

dbSNP variants (sampled 300 via entrez): RS1000433301 (9:34724666 A>C,G), RS1001490272 (9:34724071 C>A,T), RS1001836326 (9:34723802 A>G,T), RS1002021243 (9:34730742 G>C), RS1002052320 (9:34730381 T>C), RS1002082111 (9:34722934 T>C), RS1002437423 (9:34725075 A>G), RS1002898278 (9:34726000 A>C), RS1003266756 (9:34729398 T>A), RS1003316067 (9:34729779 G>C), RS1003546401 (9:34722788 A>G), RS1004164431 (9:34725016 T>A), RS1005838273 (9:34731184 T>A), RS1006129112 (9:34723476 G>A), RS1006473905 (9:34730912 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:614749

GenCC curated gene-disease

Mondo (1): hyperphosphatasia with intellectual disability syndrome 2 (MONDO:0013882)

Orphanet (1): Hyperphosphatasia-intellectual disability syndrome (Orphanet:247262)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005537_172	Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy)	6.000000e-09
GCST008839_259	Height	4.000000e-15

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
licochalcone B	increases expression	1
bisphenol S	increases methylation	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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