SPMAP1

Summary

SPMAP1 (sperm microtubule associated protein 1, HGNC:34492) is a protein-coding gene on chromosome 17q12, encoding Sperm microtubule associated protein 1 (A8MV24).

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001080465

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34492
Approved symbol	SPMAP1
Name	sperm microtubule associated protein 1
Location	17q12
Locus type	gene with protein product
Status	Approved
Aliases	LOC388381
Ensembl gene	ENSG00000275489
Ensembl biotype	protein_coding
Entrez	388381

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000614158

RefSeq mRNA: 1 — MANE Select: NM_001080465 NM_001080465

CCDS: CCDS42310

Canonical transcript exons

ENST00000614158 — 3 exons

Exon	Start	End
ENSE00003721680	38841183	38841438
ENSE00003743550	38837141	38837240
ENSE00003747777	38835086	38835346

Expression profiles

Bgee: expression breadth broad, 79 present calls, max score 87.67.

Top tissues by expression

108 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	87.67	gold quality
left testis	UBERON:0004533	85.02	gold quality
testis	UBERON:0000473	84.34	gold quality
right testis	UBERON:0004534	83.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.19	gold quality
mucosa of transverse colon	UBERON:0004991	44.87	gold quality
granulocyte	CL:0000094	43.75	silver quality
right adrenal gland cortex	UBERON:0035827	43.07	gold quality
left adrenal gland cortex	UBERON:0035825	42.71	gold quality
mucosa of stomach	UBERON:0001199	41.84	silver quality
stromal cell of endometrium	CL:0002255	41.57	silver quality
left adrenal gland	UBERON:0001234	41.10	gold quality
right lobe of thyroid gland	UBERON:0001119	40.30	silver quality
left lobe of thyroid gland	UBERON:0001120	39.71	silver quality
thyroid gland	UBERON:0002046	39.06	silver quality
adrenal gland	UBERON:0002369	38.73	gold quality
omental fat pad	UBERON:0010414	38.53	gold quality
skin of leg	UBERON:0001511	37.48	gold quality
skeletal muscle tissue	UBERON:0001134	37.22	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
adipose tissue	UBERON:0001013	37.12	gold quality
zone of skin	UBERON:0000014	36.55	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
body of pancreas	UBERON:0001150	36.45	silver quality
right adrenal gland	UBERON:0001233	36.33	gold quality
pancreas	UBERON:0001264	36.30	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
left ovary	UBERON:0002119	36.00	silver quality
adenohypophysis	UBERON:0002196	35.90	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting SPMAP1, 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-4775	99.98	75.00	6394
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-11399	98.71	65.69	869
HSA-MIR-6864-5P	98.38	66.59	1079
HSA-MIR-550A-3P	98.37	69.61	632
HSA-MIR-3179	98.22	65.90	1445
HSA-MIR-200C-5P	97.71	67.73	596
HSA-MIR-9900	96.06	65.48	557

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spmap1	ENSMUSG00000018543
rattus_norvegicus	Spmap1	ENSRNOG00000036888

Protein

Protein identifiers

Sperm microtubule associated protein 1 — A8MV24 (reviewed: A8MV24)

All UniProt accessions (1): A8MV24

RefSeq proteins (1): NP_001073934* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028027	SPMAP1	Family

Pfam: PF15075

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MV24-F1	76.44	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, GSE14415_ACT_VS_CTRL_NATURAL_TREG_UP, MIR7515, MIR6864_5P, GSE13229_MATURE_VS_INTMATURE_NKCELL_UP, GSE14308_TH2_VS_INDUCED_TREG_UP, chr17q12, NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON, GSE17974_CTRL_VS_ACT_IL4_AND_ANTI_IL12_1H_CD4_TCELL_UP, GSE20366_TREG_VS_NAIVE_CD4_TCELL_HOMEOSTATIC_CONVERSION_UP, WP_17Q12_COPY_NUMBER_VARIATION_SYNDROME, GSE19888_ADENOSINE_A3R_INH_VS_ACT_IN_MAST_CELL_DN, GSE20198_UNTREATED_VS_IL12_TREATED_ACT_CD4_TCELL_UP, GSE21546_UNSTIM_VS_ANTI_CD3_STIM_SAP1A_KO_AND_ELK1_KO_DP_THYMOCYTES_UP, GSE16385_UNTREATED_VS_12H_ROSIGLITAZONE_TREATED_MACROPHAGE_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

176 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPMAP1	C17orf50	Q8WW18	693
SPMAP1	CFAP97D1	B2RV13	582
SPMAP1	SPEM2	Q0P670	581
SPMAP1	TBC1D3K	A0A087X1G2	434
SPMAP1	KRTAP9-7	A8MTY7	433
SPMAP1	ZNF426	Q9BUY5	418
SPMAP1	CDRT15L2	A8MXV6	400
SPMAP1	ARK2C	Q6ZSG1	396
SPMAP1	TBC1D3H	P0C7X1	369
SPMAP1	KRTAP9-8	Q9BYQ0	348
SPMAP1	PYGO1	Q9Y3Y4	336
SPMAP1	TBC1D28	Q2M2D7	336
SPMAP1	OR1E2	P47887	324
SPMAP1	TBC1D3D	A0A087WVF3	323
SPMAP1	SLC35G6	P0C7Q6	312

IntAct

0 interactions, top by confidence:

BioGRID (1): C17orf98 (Affinity Capture-MS)

ESM2 similar proteins: A5CXK8, A5VIR6, A7IFY5, A7Y3E0, A8AKK2, A8MV24, A9CB83, B0YPR6, B2IK66, B8ELF9, C0R305, O06091, O83952, P07929, P0C1L9, P0DQF3, P14155, P15097, P16130, P16628, P17284, P17681, P21406, P24737, P55759, P75406, P82338, P83672, P86231, Q197F9, Q1QN26, Q23946, Q24703, Q2YDM5, Q495D7, Q5GSU8, Q6IMG9, Q6IMH0, Q6MVL6, Q73H90

Diamond homologs: A8MV24, Q9DAQ5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

377 predictions. Top by Δscore:

Variant	Effect	Δscore
17:38835345:CCCT:C	acceptor_gain	0.9900
17:38835346:CCT:C	acceptor_gain	0.9900
17:38835348:T:C	acceptor_gain	0.9900
17:38837145:C:A	donor_gain	0.9900
17:38841178:TATA:T	donor_loss	0.9900
17:38841179:ATAC:A	donor_loss	0.9900
17:38841180:TACC:T	donor_loss	0.9900
17:38841181:ACCT:A	donor_loss	0.9900
17:38841182:C:CG	donor_loss	0.9900
17:38841177:CTATA:C	donor_loss	0.9800
17:38835343:TGCC:T	acceptor_gain	0.9700
17:38835344:GCCC:G	acceptor_loss	0.9700
17:38835345:CC:C	acceptor_gain	0.9700
17:38835345:CCC:C	acceptor_loss	0.9700
17:38835346:CC:C	acceptor_loss	0.9700
17:38835347:C:T	acceptor_gain	0.9700
17:38835348:T:G	acceptor_loss	0.9700
17:38835443:G:C	donor_gain	0.9700
17:38837183:G:A	donor_gain	0.9700
17:38841212:C:CT	donor_gain	0.9700
17:38835348:T:TC	acceptor_gain	0.9600
17:38837159:T:A	donor_gain	0.9600
17:38837172:T:C	donor_gain	0.9600
17:38835344:GCC:G	acceptor_gain	0.9500
17:38835347:C:CC	acceptor_gain	0.9500
17:38837236:TGATC:T	acceptor_gain	0.9500
17:38837239:TC:T	acceptor_gain	0.9500
17:38837240:CC:C	acceptor_gain	0.9500
17:38837247:G:GC	acceptor_gain	0.9500
17:38837238:ATCCT:A	acceptor_loss	0.9400

AlphaMissense

1007 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:38841345:A:C	F15L	0.987
17:38841345:A:T	F15L	0.987
17:38841347:A:G	F15L	0.987
17:38837157:T:A	R97S	0.977
17:38837157:T:G	R97S	0.977
17:38841225:G:C	F55L	0.973
17:38841225:G:T	F55L	0.973
17:38841227:A:G	F55L	0.973
17:38835219:G:C	F145L	0.971
17:38835219:G:T	F145L	0.971
17:38835221:A:G	F145L	0.971
17:38835260:G:T	R132S	0.967
17:38841246:G:C	D48E	0.967
17:38841246:G:T	D48E	0.967
17:38837158:C:G	R97T	0.965
17:38837187:G:C	F87L	0.961
17:38837187:G:T	F87L	0.961
17:38837189:A:G	F87L	0.961
17:38841248:C:G	D48H	0.961
17:38841346:A:G	F15S	0.960
17:38835252:G:C	N134K	0.957
17:38835252:G:T	N134K	0.957
17:38835255:C:A	R133S	0.955
17:38835255:C:G	R133S	0.955
17:38841199:A:G	L64S	0.954
17:38835239:G:T	R139S	0.951
17:38841183:C:A	Q69H	0.951
17:38841183:C:G	Q69H	0.951
17:38837204:C:G	D82H	0.950
17:38835267:A:C	F129L	0.948

dbSNP variants (sampled 300 via entrez): RS1000070303 (17:38838210 A>G), RS1000088122 (17:38842730 C>T), RS1000470865 (17:38838140 C>G,T), RS1000501806 (17:38837925 G>A), RS1001001018 (17:38839850 G>A,C), RS1001503508 (17:38839237 T>C), RS1002153447 (17:38838936 A>C), RS1002752937 (17:38840450 G>A,T), RS1003017718 (17:38842742 G>A,T), RS1003458405 (17:38842362 C>T), RS1003585194 (17:38837965 T>C,G), RS1004021100 (17:38837725 G>A), RS1004023231 (17:38840519 C>T), RS1004169805 (17:38841901 G>A), RS1004586801 (17:38836114 C>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

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases methylation	1
2-methyl-4-isothiazolin-3-one	increases expression	1
tobacco tar	decreases expression	1
aflatoxin B2	increases methylation	1
Benzo(a)pyrene	increases methylation	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1
Lactic Acid	affects expression	1

Clinical trials (associated diseases)

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