SERTM1

Summary

SERTM1 (serine rich and transmembrane domain containing 1, HGNC:33792) is a protein-coding gene on chromosome 13q13.3, encoding Serine-rich and transmembrane domain-containing protein 1 (A2A2V5).

Located in intracellular membrane-bounded organelle.

Source: NCBI Gene 400120 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_203451

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33792
Approved symbol	SERTM1
Name	serine rich and transmembrane domain containing 1
Location	13q13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000180440
Ensembl biotype	protein_coding
Entrez	400120

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000315190, ENST00000914385, ENST00000914386, ENST00000941019, ENST00000941020

RefSeq mRNA: 1 — MANE Select: NM_203451 NM_203451

CCDS: CCDS9358

Canonical transcript exons

ENST00000315190 — 2 exons

Exon	Start	End
ENSE00001253754	36674020	36674184
ENSE00001253759	36694906	36697839

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 96.20.

FANTOM5 (CAGE): breadth broad, TPM avg 2.4296 / max 254.2008, expressed in 349 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134773	2.3105	341
134774	0.0998	51
134772	0.0193	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
germinal epithelium of ovary	UBERON:0001304	96.20	gold quality
left uterine tube	UBERON:0001303	94.04	gold quality
fallopian tube	UBERON:0003889	89.29	gold quality
oviduct epithelium	UBERON:0004804	89.08	gold quality
dorsal root ganglion	UBERON:0000044	86.29	gold quality
parietal pleura	UBERON:0002400	86.24	gold quality
body of uterus	UBERON:0009853	84.11	gold quality
endocervix	UBERON:0000458	83.24	gold quality
prefrontal cortex	UBERON:0000451	82.84	gold quality
Brodmann (1909) area 46	UBERON:0006483	82.60	gold quality
adenohypophysis	UBERON:0002196	82.47	gold quality
mammalian vulva	UBERON:0000997	82.44	gold quality
right uterine tube	UBERON:0001302	79.87	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	78.97	gold quality
smooth muscle tissue	UBERON:0001135	78.56	gold quality
frontal cortex	UBERON:0001870	78.34	gold quality
pituitary gland	UBERON:0000007	78.27	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.71	gold quality
neocortex	UBERON:0001950	77.25	gold quality
anterior cingulate cortex	UBERON:0009835	77.18	gold quality
cerebral cortex	UBERON:0000956	76.64	gold quality
islet of Langerhans	UBERON:0000006	76.54	gold quality
Ammon’s horn	UBERON:0001954	76.12	gold quality
myometrium	UBERON:0001296	75.21	gold quality
amygdala	UBERON:0001876	75.01	gold quality
right frontal lobe	UBERON:0002810	74.48	gold quality
temporal lobe	UBERON:0001871	74.31	gold quality
middle temporal gyrus	UBERON:0002771	74.20	gold quality
urethra	UBERON:0000057	74.16	gold quality
entorhinal cortex	UBERON:0002728	73.76	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-5061	yes	16.52
E-GEOD-81608	yes	8.66
E-ENAD-27	yes	5.33
E-HCAD-31	yes	5.08
E-GEOD-83139	yes	4.93
E-ANND-3	yes	3.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

113 targeting SERTM1, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-944	99.82	70.85	3042

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Sertm1	ENSMUSG00000056306
rattus_norvegicus	Sertm1	ENSRNOG00000014046

Protein

Protein identifiers

Serine-rich and transmembrane domain-containing protein 1 — A2A2V5 (reviewed: A2A2V5)

All UniProt accessions (1): A2A2V5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SERTM family.

RefSeq proteins (1): NP_982276* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031741	SERTM	Family

Pfam: PF15872

UniProt features (3 total): chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A2A2V5-F1	64.26	0.21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): BENPORATH_ES_WITH_H3K27ME3, MYOGENIN_Q6, chr13q13, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, MIR6867_5P, MIR4328, MIR12123, MIR6833_3P, MIR6873_3P, MIR4768_5P, MIR3609, MIR548AH_5P, MIR3919

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

874 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SERTM1	TMEM164	Q5U3C3	530
SERTM1	FAM91A1	Q658Y4	506
SERTM1	TMEM14A	Q9Y6G1	490
SERTM1	CACNG4	Q9UBN1	451
SERTM1	OR5AU1	Q8NGC0	445
SERTM1	HOOK1	Q9UJC3	433
SERTM1	KCNB2	Q92953	425
SERTM1	ST3GAL3	Q11203	422
SERTM1	SPAG5	Q96R06	421
SERTM1	TXLNA	P40222	417
SERTM1	NRN1	Q9NPD7	416
SERTM1	DENND1A	Q8TEH3	412
SERTM1	TRIQK	Q629K1	380
SERTM1	PROSER1	Q86XN7	375
SERTM1	SPOCK1	Q08629	371

IntAct

40 interactions, top by confidence:

A	B	Type	Score
SERTM1	MTIF3	psi-mi:“MI:0915”(physical association)	0.560
TMEM19	SERTM1	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	LHFPL5	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	SPACA1	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	LRRC4C	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	GJB1	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	CLDN7	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	EMP1	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	GPX8	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	GPR42	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	TMEM19	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	KCNJ6	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	CD53	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	MS4A4A	psi-mi:“MI:0915”(physical association)	0.560
SERTM1	CLDN7	psi-mi:“MI:0915”(physical association)	0.000
SERTM1	EMP1	psi-mi:“MI:0915”(physical association)	0.000
SERTM1	GPX8	psi-mi:“MI:0915”(physical association)	0.000
SERTM1	GPR42	psi-mi:“MI:0915”(physical association)	0.000
SERTM1	KCNJ6	psi-mi:“MI:0915”(physical association)	0.000
SERTM1	MS4A4A	psi-mi:“MI:0915”(physical association)	0.000
SERTM1	GJB1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), SERTM1 (Two-hybrid), CLDN7 (Two-hybrid), LHFPL5 (Two-hybrid), APP (Reconstituted Complex)

ESM2 similar proteins: A0A1B0GRQ0, A0A1B0GSN8, A0A1B0GSZ0, A0A1B0GVQ0, A0A1B0GVT2, A0A1B0GWG4, A2A2V5, A2A9G7, A2APA5, A2VE22, A6NFZ4, A6QQ93, A7E1Z1, A7MB05, A9CBA0, B7ZWI3, D3ZR35, E9Q942, F5HAK6, F5HFG3, O14668, O39519, O39920, P09312, P0DJ93, P18345, P86045, Q2KIK3, Q498C7, Q5RCB6, Q5RF07, Q5RF75, Q67593, Q68D42, Q6AXS2, Q6UWT2, Q77NN6, Q7M750, Q80WK2, Q8BGN6

Diamond homologs: A0A1B0GSN8, A0A1B0GWG4, A2A2V5, Q8CD78

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

461 predictions. Top by Δscore:

Variant	Effect	Δscore
13:36674161:G:GT	donor_gain	1.0000
13:36674161:G:T	donor_gain	1.0000
13:36674182:CAGG:C	donor_loss	0.9900
13:36674185:G:A	donor_loss	0.9900
13:36694904:A:AG	acceptor_gain	0.9900
13:36694905:G:GA	acceptor_gain	0.9900
13:36694905:GTC:G	acceptor_gain	0.9900
13:36694905:GTCT:G	acceptor_gain	0.9900
13:36694905:GTCTC:G	acceptor_gain	0.9900
13:36674185:GTCA:G	donor_gain	0.9800
13:36674188:A:AG	donor_gain	0.9800
13:36674189:G:GG	donor_gain	0.9800
13:36694901:TTCA:T	acceptor_loss	0.9800
13:36694902:TCA:T	acceptor_loss	0.9800
13:36694903:CA:C	acceptor_loss	0.9800
13:36694905:GT:G	acceptor_gain	0.9800
13:36674802:G:T	donor_gain	0.9700
13:36674181:GCAG:G	donor_gain	0.9600
13:36681036:A:G	acceptor_gain	0.9500
13:36694648:T:G	donor_gain	0.9400
13:36674195:G:T	donor_gain	0.9300
13:36674183:AGGTC:A	donor_gain	0.9200
13:36674802:G:GT	donor_gain	0.9200
13:36674762:A:T	donor_gain	0.9100
13:36681373:C:G	donor_gain	0.9100
13:36681371:G:GA	donor_gain	0.8800
13:36694174:G:GG	donor_gain	0.8800
13:36674868:G:GG	donor_gain	0.8600
13:36681035:A:AC	acceptor_gain	0.8400
13:36694066:A:AG	acceptor_gain	0.8300

AlphaMissense

674 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:36695226:A:C	S50R	0.997
13:36695228:C:A	S50R	0.997
13:36695228:C:G	S50R	0.997
13:36695224:T:C	L49P	0.986
13:36695275:T:C	L66P	0.985
13:36695220:T:C	F48L	0.983
13:36695222:C:A	F48L	0.983
13:36695222:C:G	F48L	0.983
13:36695230:T:C	L51P	0.979
13:36695266:T:C	L63P	0.978
13:36695224:T:A	L49H	0.976
13:36695224:T:G	L49R	0.976
13:36695245:T:G	L56R	0.974
13:36695230:T:G	L51R	0.972
13:36695242:T:C	L55P	0.969
13:36695242:T:G	L55R	0.969
13:36695278:A:T	K67I	0.968
13:36695236:C:A	A53E	0.967
13:36695245:T:C	L56P	0.967
13:36695218:T:A	I47K	0.966
13:36695275:T:A	L66H	0.966
13:36695230:T:A	L51H	0.964
13:36695221:T:G	F48C	0.963
13:36695263:C:A	A62D	0.960
13:36695266:T:A	L63H	0.957
13:36695221:T:C	F48S	0.956
13:36695341:C:T	T88I	0.955
13:36695233:T:C	L52S	0.952
13:36695245:T:A	L56H	0.951
13:36695218:T:G	I47R	0.950

dbSNP variants (sampled 300 via entrez): RS1000107074 (13:36681669 T>A), RS1000169550 (13:36675334 T>C), RS1000387287 (13:36687858 A>G), RS1000436425 (13:36697237 A>G), RS1000566025 (13:36673155 TA>T), RS1000626376 (13:36675047 G>C,T), RS1000924065 (13:36696884 T>C), RS1000989618 (13:36686533 G>T), RS1001232715 (13:36673898 C>A,G,T), RS1001234662 (13:36689471 C>T), RS1001296678 (13:36674123 G>A,C), RS1001336934 (13:36686790 A>C,G), RS1001370996 (13:36696452 A>T), RS1001579311 (13:36674005 C>A,G,T), RS1001666075 (13:36689739 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
GCST002928_22	Nickel levels	5.000000e-06
GCST008399_20	Cocaine dependence	2.000000e-06
GCST010307_9	Urinary albumin excretion	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004285	albuminuria

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	5
trichostatin A	increases expression	1
sodium arsenite	increases expression	1
ferrous chloride	decreases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Arsenic Trioxide	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Carbamazepine	affects expression	1
Copper	decreases expression, affects cotreatment	1
Folic Acid	increases expression	1
Nickel	decreases expression	1
Triclosan	decreases expression	1
Cyclosporine	decreases methylation	1
Asbestos, Serpentine	increases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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