SSMEM1

Summary

SSMEM1 (serine rich single-pass membrane protein 1, HGNC:29580) is a protein-coding gene on chromosome 7q32.2, encoding Serine-rich single-pass membrane protein 1 (Q8WWF3).

Predicted to be located in membrane.

Source: NCBI Gene 136263 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_145268

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29580
Approved symbol	SSMEM1
Name	serine rich single-pass membrane protein 1
Location	7q32.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40316
Ensembl gene	ENSG00000165120
Ensembl biotype	protein_coding
Entrez	136263

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000297819, ENST00000648806

RefSeq mRNA: 1 — MANE Select: NM_145268 NM_145268

CCDS: CCDS5816

Canonical transcript exons

ENST00000297819 — 3 exons

Exon	Start	End
ENSE00001090523	130207860	130208093
ENSE00001090526	130213480	130213534
ENSE00003840997	130215974	130216844

Expression profiles

Bgee: expression breadth broad, 31 present calls, max score 91.19.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0619 / max 39.4057, expressed in 6 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
81053	0.0364	5
81052	0.0255	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	91.19	gold quality
left testis	UBERON:0004533	87.03	gold quality
right testis	UBERON:0004534	86.27	gold quality
testis	UBERON:0000473	84.73	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.80	gold quality
sperm	CL:0000019	80.38	gold quality
adult organism	UBERON:0007023	70.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	59.31	gold quality
tendon of biceps brachii	UBERON:0008188	45.79	gold quality
oocyte	CL:0000023	45.72	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
skin of hip	UBERON:0001554	43.26	silver quality
secondary oocyte	CL:0000655	42.57	gold quality
vastus lateralis	UBERON:0001379	41.66	gold quality
quadriceps femoris	UBERON:0001377	41.62	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality
placenta	UBERON:0001987	40.13	silver quality
mammary duct	UBERON:0001765	40.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting SSMEM1, 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-1277-5P	100.00	73.95	5056
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-23A-5P	99.94	65.39	468
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-5582-5P	99.27	71.42	1879
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-138-2-3P	98.91	68.33	1643
HSA-MIR-4451	98.82	68.17	1455
HSA-MIR-3922-5P	98.77	66.53	1059
HSA-MIR-7705	98.69	67.47	543
HSA-MIR-4299	98.28	66.96	850
HSA-MIR-10397-3P	97.78	65.70	601

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ssmem1	ENSMUSG00000029784
rattus_norvegicus	Ssmem1	ENSRNOG00000010345

Protein

Protein identifiers

Serine-rich single-pass membrane protein 1 — Q8WWF3 (reviewed: Q8WWF3)

All UniProt accessions (3): A0A3B3ISA2, A4D1L0, Q8WWF3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_660311* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027955	DUF4636	Family

Pfam: PF15468

UniProt features (10 total): compositionally biased region 4, region of interest 3, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WWF3-F1	58.30	0.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): TGCTGAY_UNKNOWN, chr7q32, WTGAAAT_UNKNOWN, HP1SITEFACTOR_Q6, MARSON_BOUND_BY_FOXP3_STIMULATED, ZNF175_TARGET_GENES, MIR607, MIR3671, MIR1250_3P, MIR12123, MIR6504_3P, MIR10399_5P, MIR5582_5P, MIR130B_5P, MIR7161_3P

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

284 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSMEM1	SPACA1	Q9HBV2	710
SSMEM1	SPATA46	Q5T0L3	680
SSMEM1	CIB4	A0PJX0	626
SSMEM1	TSSK4	Q6SA08	608
SSMEM1	LRGUK	Q96M69	564
SSMEM1	TM9SF3	Q9HD45	544
SSMEM1	TSGA13	Q96PP4	541
SSMEM1	FAM170A	A1A519	533
SSMEM1	MTMR4	Q9NYA4	529
SSMEM1	FAM170B	A6NMN3	526
SSMEM1	VPS54	Q9P1Q0	516
SSMEM1	CFAP77	Q6ZQR2	514
SSMEM1	OR4D1	Q15615	506
SSMEM1	SPEF2	Q9C093	504
SSMEM1	DOCK11	Q5JSL3	500

IntAct

308 interactions, top by confidence:

A	B	Type	Score
TMEM144	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
GET3	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
EHHADH	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
SLC30A8	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
SLC35A4	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
SLC30A2	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
CSGALNACT2	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
UNC93B1	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
SLC39A9	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
CCL4L1	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
C5	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
GPR151	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
C1QL4	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
STX8	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560
SSMEM1	SLC38A1	psi-mi:“MI:0915”(physical association)	0.560
NRM	SSMEM1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (124): SMAD5 (Affinity Capture-MS), CSNK1A1 (Affinity Capture-MS), NSUN4 (Affinity Capture-MS), CSNK1E (Affinity Capture-MS), NDUFV3 (Affinity Capture-MS), CSNK1D (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), SPCS1 (Affinity Capture-MS), NDUFA7 (Affinity Capture-MS), CKAP4 (Affinity Capture-MS), STOM (Affinity Capture-MS), SSMEM1 (Two-hybrid), SSMEM1 (Two-hybrid), SSMEM1 (Two-hybrid), SSMEM1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVH6, A0A1L8FZ84, A0A2K1J5A5, A0A2K1JJ00, A4IGV6, B3DHS1, O94243, O95561, P03209, P04605, P05909, P17759, P18098, P22051, P24109, P24433, P32845, Q00039, Q03233, Q03937, Q06616, Q09824, Q0VCV7, Q12418, Q13352, Q19541, Q1T763, Q3KPS4, Q5R5R7, Q5RD08, Q5XHY8, Q5XIU7, Q6AXY9, Q6DFB0, Q703I1, Q759B7, Q8N9R6, Q8TAL5, Q8WWF3, Q95JJ2

Diamond homologs: Q4R309, Q8WWF3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 101 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Transport of small molecules	10	4.7×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

519 predictions. Top by Δscore:

Variant	Effect	Δscore
7:130208026:G:GT	donor_gain	0.9900
7:130215972:A:AG	acceptor_gain	0.9900
7:130215973:G:GG	acceptor_gain	0.9900
7:130215973:GCAA:G	acceptor_gain	0.9900
7:130215962:ATT:A	acceptor_gain	0.9700
7:130215973:GCA:G	acceptor_gain	0.9700
7:130215964:T:TA	acceptor_gain	0.9600
7:130215962:ATTG:A	acceptor_gain	0.9400
7:130215970:TTA:T	acceptor_loss	0.9300
7:130215973:G:GC	acceptor_loss	0.9300
7:130215975:A:AG	acceptor_gain	0.9300
7:130215973:GC:G	acceptor_gain	0.9200
7:130207938:G:T	donor_gain	0.9100
7:130215976:A:G	acceptor_gain	0.9100
7:130207938:G:GT	donor_gain	0.8900
7:130215965:G:A	acceptor_gain	0.8800
7:130215968:T:A	acceptor_gain	0.8700
7:130207942:T:TA	donor_gain	0.8600
7:130207943:A:AA	donor_gain	0.8600
7:130215963:T:G	acceptor_gain	0.8500
7:130207945:A:G	donor_gain	0.8100
7:130208321:G:GG	donor_gain	0.8100
7:130207914:G:GT	donor_gain	0.8000
7:130213479:GAT:G	acceptor_gain	0.8000
7:130208044:ATTT:A	donor_gain	0.7900
7:130208045:TTTT:T	donor_gain	0.7900
7:130208046:T:G	donor_gain	0.7900
7:130210622:GTGT:G	donor_gain	0.7900
7:130210623:TGTT:T	donor_gain	0.7900
7:130215962:A:AG	acceptor_gain	0.7900

AlphaMissense

1649 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:130208040:T:A	W44R	0.934
7:130208040:T:C	W44R	0.934
7:130216362:G:C	W209C	0.927
7:130216362:G:T	W209C	0.927
7:130207932:T:C	F8L	0.925
7:130207934:T:A	F8L	0.925
7:130207934:T:G	F8L	0.925
7:130216360:T:A	W209R	0.888
7:130216360:T:C	W209R	0.888
7:130208043:T:G	Y45D	0.878
7:130208043:T:C	Y45H	0.872
7:130216221:G:C	W162C	0.843
7:130216221:G:T	W162C	0.843
7:130216341:A:C	K202N	0.843
7:130216341:A:T	K202N	0.843
7:130208046:T:C	F46L	0.834
7:130208048:T:A	F46L	0.834
7:130208048:T:G	F46L	0.834
7:130208035:T:C	L42P	0.833
7:130208031:T:C	F41L	0.827
7:130208033:C:A	F41L	0.827
7:130208033:C:G	F41L	0.827
7:130207937:G:C	W9C	0.826
7:130207937:G:T	W9C	0.826
7:130216336:T:A	C201S	0.821
7:130216337:G:C	C201S	0.821
7:130208035:T:G	L42R	0.818
7:130216224:G:C	K163N	0.808
7:130216224:G:T	K163N	0.808
7:130208056:T:A	V49E	0.807

dbSNP variants (sampled 300 via entrez): RS1000902557 (7:130210428 A>G), RS1000915473 (7:130210009 C>G), RS1000921487 (7:130211009 A>C), RS1001107036 (7:130204833 TAA>T), RS1001372383 (7:130212972 C>T), RS1001546663 (7:130204163 T>A), RS1002144544 (7:130205383 G>A,C,T), RS1002209210 (7:130206358 A>G,T), RS1002514326 (7:130214505 C>A), RS1002731499 (7:130207595 A>C), RS1002982330 (7:130213880 C>T), RS1003039438 (7:130214438 A>T), RS1003104526 (7:130206775 A>G), RS1003493688 (7:130208353 C>G), RS1003566153 (7:130206368 A>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

1 associations (top):

Study	Trait	p-value
GCST008478_64	Neurological blood protein biomarker levels	9.000000e-15

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
Am 580	decreases expression	1
Rosiglitazone	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Endosulfan	affects cotreatment, decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Phthalic Acids	decreases methylation	1
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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