SPMAP2L

Summary

SPMAP2L (sperm microtubule associated protein 2 like, HGNC:43771) is a protein-coding gene on chromosome 4q12, encoding Sperm microtubule associated protein 2-like (P0DJG4).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001256475

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:43771
Approved symbol	SPMAP2L
Name	sperm microtubule associated protein 2 like
Location	4q12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000249693
Ensembl biotype	protein_coding
Entrez	100506564

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000510716, ENST00000512175

RefSeq mRNA: 1 — MANE Select: NM_001256475 NM_001256475

CCDS: CCDS58899

Canonical transcript exons

ENST00000512175 — 9 exons

Exon	Start	End
ENSE00002041840	56600934	56601109
ENSE00002042402	56552549	56552614
ENSE00002061501	56603209	56603507
ENSE00002072638	56596500	56596631
ENSE00002081975	56530606	56531169
ENSE00002082961	56548790	56548823
ENSE00003487065	56584497	56584611
ENSE00003497328	56559392	56559520
ENSE00003522740	56575505	56575642

Expression profiles

Bgee: expression breadth broad, 56 present calls, max score 85.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3235 / max 39.9712, expressed in 146 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
47739	0.3235	146

Top tissues by expression

106 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	85.24	gold quality
left testis	UBERON:0004533	66.95	gold quality
right testis	UBERON:0004534	66.87	gold quality
testis	UBERON:0000473	66.83	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	56.34	gold quality
smooth muscle tissue	UBERON:0001135	51.61	gold quality
urinary bladder	UBERON:0001255	51.14	gold quality
gall bladder	UBERON:0002110	49.69	gold quality
stromal cell of endometrium	CL:0002255	48.74	gold quality
muscle layer of sigmoid colon	UBERON:0035805	46.73	gold quality
bone marrow	UBERON:0002371	45.80	silver quality
islet of Langerhans	UBERON:0000006	44.58	gold quality
ventricular zone	UBERON:0003053	43.89	silver quality
bone marrow cell	CL:0002092	43.82	gold quality
myometrium	UBERON:0001296	41.56	gold quality
ectocervix	UBERON:0012249	40.50	gold quality
body of uterus	UBERON:0009853	40.17	gold quality
vagina	UBERON:0000996	39.81	silver quality
uterine cervix	UBERON:0000002	39.70	silver quality
muscle tissue	UBERON:0002385	39.46	gold quality
skin of leg	UBERON:0001511	39.30	gold quality
zone of skin	UBERON:0000014	38.37	gold quality
descending thoracic aorta	UBERON:0002345	37.97	silver quality
colon	UBERON:0001155	37.89	gold quality
ascending aorta	UBERON:0001496	37.36	silver quality
fundus of stomach	UBERON:0001160	37.33	gold quality
ganglionic eminence	UBERON:0004023	37.33	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
thoracic aorta	UBERON:0001515	37.10	silver quality
skin of abdomen	UBERON:0001416	36.50	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.40

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spmap2l	ENSMUSG00000029248
rattus_norvegicus	Spmap2l	ENSRNOG00000002085
drosophila_melanogaster	Theg	FBGN0038921

Paralogs (1): SPMAP2 (ENSG00000105549)

Protein

Protein identifiers

Sperm microtubule associated protein 2-like — P0DJG4 (reviewed: P0DJG4)

Alternative names: Testicular haploid expressed gene protein-like, Theg spermatid-like protein

All UniProt accessions (1): P0DJG4

RefSeq proteins (1): NP_001243404* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006623	THEG	Repeat
IPR042401	SPMAP2-like	Family

Pfam: PF14912

UniProt features (14 total): repeat 8, compositionally biased region 3, chain 1, sequence conflict 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DJG4-F1	63.18	0.11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, chr4q12, ZWANG_EGF_PERSISTENTLY_UP, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_UP, DESCARTES_MAIN_FETAL_ERYTHROBLASTS, DESCARTES_FETAL_ADRENAL_ERYTHROBLASTS, DESCARTES_FETAL_KIDNEY_ERYTHROBLASTS, DESCARTES_FETAL_LIVER_ERYTHROBLASTS, PULVER_FOREY_CELLCYCLE_PEAKING_G1_S, GSE7460_FOXP3_MUT_VS_HET_ACT_TCONV_UP, GSE7460_CTRL_VS_FOXP3_OVEREXPR_TCONV_UP, GSE6674_UNSTIM_VS_ANTI_IGM_STIM_BCELL_DN, GSE23925_LIGHT_ZONE_VS_NAIVE_BCELL_UP, GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_UP, GSE25123_CTRL_VS_ROSIGLITAZONE_STIM_MACROPHAGE_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

146 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPMAP2L	CFAP61	Q8NHU2	626
SPMAP2L	SUN3	Q8TAQ9	528
SPMAP2L	TMOD2	Q9NZR1	464
SPMAP2L	RALGAPA2	Q2PPJ7	441
SPMAP2L	AEBP1	Q8IUX7	374
SPMAP2L	TEX14	Q8IWB6	356
SPMAP2L	ZPBP	Q9BS86	348
SPMAP2L	TMOD3	Q9NYL9	346
SPMAP2L	ZP1	P60852	328
SPMAP2L	KCNH5	Q8NCM2	318
SPMAP2L	NPIPB15	A6NHN6	313
SPMAP2L	PRSS50	Q9UI38	306
SPMAP2L	XPO4	Q9C0E2	305
SPMAP2L	SLC19A3	Q9BZV2	300
SPMAP2L	ZSCAN32	Q9NX65	299

IntAct

0 interactions, top by confidence:

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

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: P0DJG4, Q5PQR6, Q9DA15

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1498 predictions. Top by Δscore:

Variant	Effect	Δscore
4:56531106:G:GG	donor_gain	1.0000
4:56531165:GGGTG:G	donor_gain	1.0000
4:56531166:GGTGG:G	donor_gain	1.0000
4:56584491:A:AG	acceptor_gain	1.0000
4:56584492:T:G	acceptor_gain	1.0000
4:56584495:A:AG	acceptor_gain	1.0000
4:56584496:G:GA	acceptor_gain	1.0000
4:56584612:G:GG	donor_gain	1.0000
4:56596627:GTCCT:G	donor_gain	1.0000
4:56596632:G:GG	donor_gain	1.0000
4:56600932:A:T	acceptor_loss	1.0000
4:56600933:G:GA	acceptor_loss	1.0000
4:56531167:GTG:G	donor_gain	0.9900
4:56584488:T:TA	acceptor_gain	0.9900
4:56584492:TATA:T	acceptor_loss	0.9900
4:56584493:ATAG:A	acceptor_loss	0.9900
4:56584494:TAGA:T	acceptor_loss	0.9900
4:56584495:A:G	acceptor_loss	0.9900
4:56584496:GA:G	acceptor_gain	0.9900
4:56584496:GAC:G	acceptor_gain	0.9900
4:56584496:GACC:G	acceptor_gain	0.9900
4:56584608:AAAA:A	donor_gain	0.9900
4:56584608:AAAAG:A	donor_loss	0.9900
4:56584609:AAA:A	donor_gain	0.9900
4:56584609:AAAG:A	donor_loss	0.9900
4:56584610:AA:A	donor_gain	0.9900
4:56584610:AAGTA:A	donor_loss	0.9900
4:56584611:AGTAA:A	donor_loss	0.9900
4:56584612:G:A	donor_loss	0.9900
4:56584613:T:TG	donor_loss	0.9900

AlphaMissense

3014 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:56596563:G:C	A347P	0.967
4:56596564:C:A	A347D	0.961
4:56603246:T:C	F441L	0.951
4:56603248:T:A	F441L	0.951
4:56603248:T:G	F441L	0.951
4:56559402:T:A	W202R	0.950
4:56559402:T:C	W202R	0.950
4:56600985:G:C	A387P	0.948
4:56559404:G:C	W202C	0.933
4:56559404:G:T	W202C	0.933
4:56559413:A:C	Q205H	0.929
4:56559413:A:T	Q205H	0.929
4:56596561:T:C	L346P	0.919
4:56596580:G:C	K352N	0.919
4:56596580:G:T	K352N	0.919
4:56600935:T:A	V370E	0.914
4:56559410:T:A	N204K	0.908
4:56559410:T:G	N204K	0.908
4:56584565:T:C	L310P	0.906
4:56559430:T:A	V211D	0.904
4:56601093:G:C	A423P	0.904
4:56596550:A:C	R342S	0.897
4:56596550:A:T	R342S	0.897
4:56552598:T:A	W193R	0.892
4:56552598:T:C	W193R	0.892
4:56596627:G:C	R368P	0.891
4:56600986:C:A	A387E	0.887
4:56603290:G:C	R455S	0.877
4:56603290:G:T	R455S	0.877
4:56559405:G:A	G203R	0.875

dbSNP variants (sampled 300 via entrez): RS10000144 (4:56543897 T>A,G), RS1000021130 (4:56606028 A>C,G), RS10000346 (4:56583157 C>T), RS1000053741 (4:56555869 A>G), RS1000054544 (4:56563617 A>C), RS1000104663 (4:56563837 T>A), RS1000111250 (4:56610694 A>G), RS1000120421 (4:56570633 G>C), RS1000191174 (4:56572012 A>G), RS1000241587 (4:56616959 T>C), RS1000274721 (4:56557171 C>T), RS1000308522 (4:56534046 C>A), RS1000317072 (4:56558049 A>G), RS1000400222 (4:56582786 A>G), RS1000415999 (4:56550313 C>T)

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

1 associations (top):

Study	Trait	p-value
GCST002936_16	Cadmium levels	9.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aflatoxin B2	decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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