SPMAP2

Summary

SPMAP2 (sperm microtubule associated protein 2, HGNC:13706) is a protein-coding gene on chromosome 19p13.3, encoding Sperm microtubule associated protein 2 (Q9P2T0). May be involved (but not essential) in spermatogenesis.

This gene is specifically expressed in the nucleus of haploid male germ cells. The orthologous gene in mice encodes a protein that may play a role in protein assembly through interactions with T-complex protein 1 subunit epsilon. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 51298 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 108 total
• MANE Select transcript: NM_016585

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13706
Approved symbol	SPMAP2
Name	sperm microtubule associated protein 2
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	CT56, THEG1
Ensembl gene	ENSG00000105549
Ensembl biotype	protein_coding
OMIM	609503
Entrez	51298

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000342640, ENST00000346878, ENST00000528213, ENST00000530711

RefSeq mRNA: 2 — MANE Select: NM_016585 NM_016585, NM_199202

CCDS: CCDS12025, CCDS12026

Canonical transcript exons

ENST00000342640 — 8 exons

Exon	Start	End
ENSE00000836249	373940	374011
ENSE00000836250	374299	374421
ENSE00001395673	375663	376026
ENSE00002164408	361747	362426
ENSE00003490626	373470	373531
ENSE00003566861	372631	372700
ENSE00003580624	367065	367224
ENSE00003675383	371205	371322

Expression profiles

Bgee: expression breadth broad, 62 present calls, max score 89.36.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1963 / max 39.3548, expressed in 94 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177879	0.0761	54
177880	0.0535	33
177881	0.0426	27
177883	0.0195	3
177882	0.0045	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	89.36	gold quality
right testis	UBERON:0004534	88.87	gold quality
testis	UBERON:0000473	85.40	gold quality
sperm	CL:0000019	80.12	silver quality
male germ cell	CL:0000015	79.45	silver quality
tongue squamous epithelium	UBERON:0006919	69.78	gold quality
olfactory bulb	UBERON:0002264	67.80	gold quality
type B pancreatic cell	CL:0000169	67.51	gold quality
triceps brachii	UBERON:0001509	67.14	gold quality
gluteal muscle	UBERON:0002000	66.98	gold quality
cervix epithelium	UBERON:0004801	61.67	gold quality
epithelial cell of pancreas	CL:0000083	60.77	gold quality
metanephric glomerulus	UBERON:0004736	59.88	gold quality
nephron tubule	UBERON:0001231	59.66	gold quality
mucosa of urinary bladder	UBERON:0001259	58.31	gold quality
adult organism	UBERON:0007023	57.41	silver quality
diaphragm	UBERON:0001103	57.32	gold quality
skin of leg	UBERON:0001511	56.34	gold quality
skin of abdomen	UBERON:0001416	55.73	gold quality
quadriceps femoris	UBERON:0001377	55.43	gold quality
vastus lateralis	UBERON:0001379	55.34	gold quality
oviduct epithelium	UBERON:0004804	55.33	gold quality
prefrontal cortex	UBERON:0000451	54.88	gold quality
zone of skin	UBERON:0000014	54.28	gold quality
kidney epithelium	UBERON:0004819	54.15	gold quality
right frontal lobe	UBERON:0002810	52.93	gold quality
Brodmann (1909) area 9	UBERON:0013540	52.67	gold quality
amniotic fluid	UBERON:0000173	52.13	gold quality
frontal cortex	UBERON:0001870	51.58	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	51.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting SPMAP2, 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-5193	100.00	67.26	1744
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-609	99.82	64.26	505
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-320A-5P	98.88	66.75	1248
HSA-MIR-1248	98.47	67.54	1314
HSA-MIR-6804-5P	98.39	65.77	1084
HSA-MIR-6854-5P	96.77	65.96	848

Literature-anchored findings (GeneRIF, showing 2)

• Functional analysis of the mouse counterpart. (PMID:10747865)
• Functional analysis of the mouse counterpart. (PMID:12748127)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	spmap2	ENSDARG00000078644
mus_musculus	Spmap2	ENSMUSG00000020317
rattus_norvegicus	Spmap2	ENSRNOG00000007960
drosophila_melanogaster	Theg	FBGN0038921

Paralogs (1): SPMAP2L (ENSG00000249693)

Protein

Protein identifiers

Sperm microtubule associated protein 2 — Q9P2T0 (reviewed: Q9P2T0)

Alternative names: Cancer/testis antigen 56, Testicular haploid expressed gene protein

All UniProt accessions (2): Q9P2T0, U3KQD4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved (but not essential) in spermatogenesis.

Subunit / interactions. Interacts with CCT5.

Subcellular location. Nucleus.

Tissue specificity. Testis specific.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9P2T0-1	1, THEG major	yes
Q9P2T0-2	2, THEG minor

RefSeq proteins (2): NP_057669, NP_954672 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006623	THEG	Repeat
IPR042401	SPMAP2-like	Family

Pfam: PF14912

UniProt features (20 total): repeat 6, compositionally biased region 5, sequence variant 4, region of interest 2, chain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2T0-F1	60.29	0.14

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 295

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): MODULE_255, MODULE_317, GOBP_MALE_GAMETE_GENERATION, GOBP_CHAPERONE_MEDIATED_PROTEIN_COMPLEX_ASSEMBLY, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, MODULE_69, chr19p13, MATZUK_SPERMATID_DIFFERENTIATION, MATZUK_SPERMATOZOA, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, MODULE_37, IL21_UP.V1_DN, KMT2D_TARGET_GENES, MIR548AW, MODULE_532

GO Biological Process (3): spermatogenesis (GO:0007283), cell differentiation (GO:0030154), chaperone-mediated protein complex assembly (GO:0051131)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

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
protein-containing complex assembly	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

450 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPMAP2	CCT5	P48643	952
SPMAP2	CT62	P0C5K7	583
SPMAP2	PRSS54	Q6PEW0	571
SPMAP2	DNAJC28	Q9NX36	497
SPMAP2	SPACA3	Q8IXA5	472
SPMAP2	ACRBP	Q8NEB7	469
SPMAP2	SPATA12	Q7Z6I5	443
SPMAP2	R3HDM4	Q96D70	436
SPMAP2	NEIL3	Q8TAT5	428
SPMAP2	ZNF165	P49910	419
SPMAP2	CIMAP1D	Q3SX64	417
SPMAP2	SPA17	Q15506	416
SPMAP2	SPANXN4	Q5MJ08	414
SPMAP2	RBM46	Q8TBY0	397
SPMAP2	CNPY4	Q8N129	388

IntAct

22 interactions, top by confidence:

A	B	Type	Score
FHL3	SPMAP2	psi-mi:“MI:0915”(physical association)	0.670
MDFI	SPMAP2	psi-mi:“MI:0915”(physical association)	0.620
SPMAP2	DR1	psi-mi:“MI:0915”(physical association)	0.560
SPMAP2	GSN	psi-mi:“MI:0915”(physical association)	0.560
SPMAP2	HIP1	psi-mi:“MI:0915”(physical association)	0.560
SPMAP2	LAMP2	psi-mi:“MI:0915”(physical association)	0.560
SPMAP2	PRICKLE3	psi-mi:“MI:0914”(association)	0.350
IKBIP	SERPINB9	psi-mi:“MI:0914”(association)	0.350
SPMAP2	FHL3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): THEG (Two-hybrid), THEG (Two-hybrid), FHL3 (Two-hybrid), CCT5 (Two-hybrid), TTL (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), MID1IP1 (Affinity Capture-MS), RPGRIP1L (Affinity Capture-MS), THEG (Affinity Capture-MS), PRICKLE3 (Affinity Capture-MS), PPP2R2D (Affinity Capture-MS), MTA2 (Affinity Capture-MS), THEG (Affinity Capture-Western), MDFI (Two-hybrid)

ESM2 similar proteins: A6H8Z2, A8T6P4, B0S4Q5, D3Z6S9, F1N4E5, F6QRE9, O35181, P0DJG4, P56950, P56975, Q05C16, Q13772, Q2KJH5, Q5FWP7, Q5JTV8, Q5PQN4, Q5PQR6, Q5PQX1, Q5R7A3, Q5RC32, Q5RD75, Q5U4H9, Q5W0A0, Q5XHX8, Q5XI03, Q5XX13, Q62187, Q66H34, Q66HD8, Q68D51, Q6A098, Q6ZPR1, Q7L0X2, Q7Z7G1, Q802X2, Q80VH0, Q8BVV7, Q8C627, Q8NDB2, Q96GE4

Diamond homologs: Q5XHX8, Q9JMB1, Q9P2T0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	96
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1354 predictions. Top by Δscore:

Variant	Effect	Δscore
19:367059:A:AC	donor_gain	1.0000
19:367060:C:CC	donor_gain	1.0000
19:367060:CTTA:C	donor_gain	1.0000
19:367063:A:AC	donor_gain	1.0000
19:367063:ACTGG:A	donor_gain	1.0000
19:367064:C:CT	donor_gain	1.0000
19:367064:CTGG:C	donor_gain	1.0000
19:367064:CTGGC:C	donor_gain	1.0000
19:367224:CCT:C	acceptor_loss	1.0000
19:367225:C:CA	acceptor_loss	1.0000
19:367226:T:C	acceptor_loss	1.0000
19:372699:CGCTA:C	acceptor_gain	1.0000
19:375660:CA:C	donor_loss	1.0000
19:362423:GGCC:G	acceptor_gain	0.9900
19:362424:GCCC:G	acceptor_loss	0.9900
19:362425:CC:C	acceptor_gain	0.9900
19:362426:CC:C	acceptor_gain	0.9900
19:362427:C:CC	acceptor_gain	0.9900
19:362428:T:C	acceptor_loss	0.9900
19:362430:G:GC	acceptor_gain	0.9900
19:367064:CTG:C	donor_gain	0.9900
19:367222:CAC:C	acceptor_gain	0.9900
19:367225:C:CC	acceptor_gain	0.9900
19:372696:CACCG:C	acceptor_gain	0.9900
19:372698:CCG:C	acceptor_gain	0.9900
19:372699:CG:C	acceptor_gain	0.9900
19:372701:C:CC	acceptor_gain	0.9900
19:372703:A:C	acceptor_gain	0.9900
19:374419:CGG:C	acceptor_gain	0.9900
19:374420:G:T	acceptor_gain	0.9900

AlphaMissense

2467 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:362341:G:C	S333R	0.973
19:362341:G:T	S333R	0.973
19:362343:T:G	S333R	0.973
19:362321:G:T	A340D	0.971
19:362322:C:G	A340P	0.967
19:362379:A:G	W321R	0.965
19:362379:A:T	W321R	0.965
19:362377:C:A	W321C	0.964
19:362377:C:G	W321C	0.964
19:373518:A:G	W173R	0.962
19:373518:A:T	W173R	0.962
19:373516:C:A	W173C	0.960
19:373516:C:G	W173C	0.960
19:367067:G:T	A304D	0.959
19:371251:G:T	A236D	0.956
19:367068:C:G	A304P	0.952
19:371252:C:G	A236P	0.952
19:373504:G:C	F177L	0.952
19:373504:G:T	F177L	0.952
19:373506:A:G	F177L	0.952
19:367166:A:G	L271S	0.951
19:372676:A:G	L197P	0.951
19:367202:G:T	A259D	0.948
19:372657:G:C	F203L	0.945
19:372657:G:T	F203L	0.945
19:372659:A:G	F203L	0.945
19:367070:A:G	L303S	0.941
19:362419:T:A	K307N	0.939
19:362419:T:G	K307N	0.939
19:362345:G:T	A332D	0.935

dbSNP variants (sampled 300 via entrez): RS1000184247 (19:367533 T>C), RS1000368630 (19:371419 T>C), RS1000417116 (19:373271 C>G,T), RS1000702549 (19:370669 G>A), RS1000760372 (19:366357 C>A,T), RS1000919382 (19:366542 C>T), RS1000959141 (19:377997 G>A), RS1001012789 (19:365947 C>T), RS1001355335 (19:370382 C>T), RS1001532561 (19:363836 C>T), RS1001700767 (19:367798 C>T), RS1001709068 (19:367964 G>A), RS1001719013 (19:364205 C>T), RS1001930789 (19:369553 G>A), RS1002077608 (19:366985 C>A,T)

Disease associations

OMIM: gene MIM:609503 | 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

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	decreases expression, affects expression, decreases reaction	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, increases methylation	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Estradiol	increases expression	1
Nickel	affects expression, decreases reaction	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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