TMEM248

Summary

TMEM248 (transmembrane protein 248, HGNC:25476) is a protein-coding gene on chromosome 7q11.21, encoding Transmembrane protein 248 (Q9NWD8).

Predicted to be located in membrane.

Source: NCBI Gene 55069 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_017994

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25476
Approved symbol	TMEM248
Name	transmembrane protein 248
Location	7q11.21
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10099, FLJ13090
Ensembl gene	ENSG00000106609
Ensembl biotype	protein_coding
Entrez	55069

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 29 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000341567, ENST00000413593, ENST00000418375, ENST00000424964, ENST00000433271, ENST00000484751, ENST00000607045, ENST00000885222, ENST00000885223, ENST00000885224, ENST00000885225, ENST00000885226, ENST00000885227, ENST00000885228, ENST00000885229, ENST00000885230, ENST00000885231, ENST00000885232, ENST00000885233, ENST00000885234, ENST00000885235, ENST00000885236, ENST00000885237, ENST00000926665, ENST00000926666, ENST00000926667, ENST00000926668, ENST00000926669, ENST00000926670, ENST00000961463, ENST00000961464

RefSeq mRNA: 1 — MANE Select: NM_017994 NM_017994

CCDS: CCDS5536

Canonical transcript exons

ENST00000341567 — 7 exons

Exon	Start	End
ENSE00000976834	66944976	66945261
ENSE00001385462	66941848	66942024
ENSE00001486440	66921225	66921461
ENSE00001682203	66955502	66958551
ENSE00001700077	66950952	66951135
ENSE00003578723	66953226	66953369
ENSE00003609318	66948544	66948694

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 98.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 76.5675 / max 505.7435, expressed in 1827 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
78890	73.9365	1826
78891	1.8753	1012
78892	0.5419	276
78893	0.1283	22
78895	0.0856	37

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	98.69	gold quality
tendon of biceps brachii	UBERON:0008188	96.99	gold quality
stromal cell of endometrium	CL:0002255	96.76	gold quality
colonic epithelium	UBERON:0000397	96.41	gold quality
cartilage tissue	UBERON:0002418	95.77	gold quality
oocyte	CL:0000023	95.44	gold quality
gall bladder	UBERON:0002110	95.38	gold quality
rectum	UBERON:0001052	95.11	gold quality
tendon	UBERON:0000043	94.95	gold quality
right lung	UBERON:0002167	94.82	gold quality
thoracic aorta	UBERON:0001515	94.78	gold quality
ascending aorta	UBERON:0001496	94.76	gold quality
descending thoracic aorta	UBERON:0002345	94.74	gold quality
endocervix	UBERON:0000458	94.71	gold quality
bone marrow cell	CL:0002092	94.62	gold quality
aorta	UBERON:0000947	94.51	gold quality
right coronary artery	UBERON:0001625	94.51	gold quality
decidua	UBERON:0002450	94.51	gold quality
calcaneal tendon	UBERON:0003701	94.51	gold quality
left uterine tube	UBERON:0001303	94.44	gold quality
duodenum	UBERON:0002114	94.43	gold quality
popliteal artery	UBERON:0002250	94.36	gold quality
tibial artery	UBERON:0007610	94.36	gold quality
smooth muscle tissue	UBERON:0001135	94.35	gold quality
left ovary	UBERON:0002119	94.34	gold quality
right ovary	UBERON:0002118	94.33	gold quality
body of uterus	UBERON:0009853	94.31	gold quality
body of pancreas	UBERON:0001150	94.22	gold quality
ectocervix	UBERON:0012249	94.17	gold quality
islet of Langerhans	UBERON:0000006	94.15	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-6524	no	89.96
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

188 targeting TMEM248, 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-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6835-3P	99.93	70.49	2904

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem248	ENSDARG00000018825
mus_musculus	Tmem248	ENSMUSG00000053094
rattus_norvegicus	Tmem248	ENSRNOG00000000893

Paralogs (1): TMEM219 (ENSG00000149932)

Protein

Protein identifiers

Transmembrane protein 248 — Q9NWD8 (reviewed: Q9NWD8)

All UniProt accessions (5): Q9NWD8, C9J3C8, C9JKP5, F8WE75, U3KQ21

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the TMEM248 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NWD8-1	1	yes
Q9NWD8-2	2

RefSeq proteins (1): NP_060464* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039493	TMEM248/TMEM219	Family
IPR039587	TMEM248/TMEM219_dom	Domain

Pfam: PF14940

UniProt features (10 total): transmembrane region 4, splice variant 2, chain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NWD8-F1	72.26	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 217 (showing top): GCACCTT_MIR18A_MIR18B, MODULE_255, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, MODULE_317, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, CATTTCA_MIR203, AAAGACA_MIR511, MORI_PLASMA_CELL_UP, chr7q11, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, ACEVEDO_LIVER_CANCER_UP, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR

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

476 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM248	M0R082	M0R082	602
TMEM248	LCN12	Q6JVE5	581
TMEM248	VKORC1L1	Q8N0U8	573
TMEM248	IBTK	Q9P2D0	507
TMEM248	ZNF469	Q96JG9	506
TMEM248	OR8H1	Q8NGG4	505
TMEM248	TENT5A	Q96IP4	479
TMEM248	GLT8D2	Q9H1C3	479
TMEM248	LRRC72	A6NJI9	474
TMEM248	CHSY1	Q86X52	452
TMEM248	COL8A2	P25067	448
TMEM248	OR6N1	Q8NGY5	447
TMEM248	OR2L2	Q8NH16	446
TMEM248	ARHGAP20	Q9P2F6	445
TMEM248	OR13F1	Q8NGS4	431

IntAct

89 interactions, top by confidence:

A	B	Type	Score
SYNE4	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
TMEM248	SYNE4	psi-mi:“MI:0915”(physical association)	0.560
C2CD2L	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
YIPF1	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
SYS1	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
RUSF1	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
TMEM248	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
MALL	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
CLDN19	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
SLC35B2	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
ARLN	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
LEPROTL1	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
FAM3C	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
TMEM147	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
ARL6IP1	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
VSTM1	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
ANKRD46	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
GPR25	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
MAL	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
LHFPL5	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
SLC41A1	TMEM248	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (65): SYNE4 (Two-hybrid), TMEM248 (Affinity Capture-MS), TMEM248 (Synthetic Lethality), ABCA2 (Affinity Capture-MS), AUP1 (Affinity Capture-MS), PKD2 (Affinity Capture-MS), PZP (Affinity Capture-MS), ROBO2 (Affinity Capture-MS), RRM2 (Affinity Capture-MS), TAF1 (Affinity Capture-MS), BCL7B (Affinity Capture-MS), CEP162 (Affinity Capture-MS), KIF21B (Affinity Capture-MS), UQCRQ (Affinity Capture-MS), VPS4A (Affinity Capture-MS)

ESM2 similar proteins: A0A0A6YXX9, A0A1Z2R986, A2RTF1, C6KI89, E9Q355, F5HFJ7, O36400, P03425, P04853, P09258, P09728, P0DP43, P12554, P12556, P16772, P19758, P21526, P22229, P28907, P35740, P35771, Q04547, Q2TAV2, Q2YDM0, Q3TBN1, Q499E0, Q4R6B2, Q5BKX0, Q5E9L2, Q5RDR5, Q66000, Q66001, Q68FB2, Q6AY76, Q6DFY8, Q6ZRH7, Q76B58, Q77MP7, Q77NN4, Q783Y1

Diamond homologs: Q2TAV2, Q2YDM0, Q3TBN1, Q5BKX0, Q68FB2, Q6AY76, Q9NWD8

SIGNOR signaling

0 interactions.

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	27
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1596 predictions. Top by Δscore:

Variant	Effect	Δscore
7:66921381:G:GG	donor_gain	1.0000
7:66941842:TTTCA:T	acceptor_loss	1.0000
7:66941843:TTCAG:T	acceptor_loss	1.0000
7:66941845:CA:C	acceptor_loss	1.0000
7:66941846:A:AG	acceptor_gain	1.0000
7:66941846:AGGT:A	acceptor_gain	1.0000
7:66941846:AGGTG:A	acceptor_gain	1.0000
7:66941847:G:GA	acceptor_gain	1.0000
7:66941847:G:T	acceptor_loss	1.0000
7:66941847:GGT:G	acceptor_gain	1.0000
7:66941847:GGTG:G	acceptor_gain	1.0000
7:66941847:GGTGG:G	acceptor_gain	1.0000
7:66941942:GC:G	donor_gain	1.0000
7:66941998:GAGAT:G	donor_gain	1.0000
7:66942022:GAG:G	donor_gain	1.0000
7:66942024:GGT:G	donor_loss	1.0000
7:66942026:T:G	donor_loss	1.0000
7:66944964:A:AG	acceptor_gain	1.0000
7:66944965:C:G	acceptor_gain	1.0000
7:66944971:CAAAG:C	acceptor_loss	1.0000
7:66944972:A:AG	acceptor_gain	1.0000
7:66944972:AAAG:A	acceptor_gain	1.0000
7:66944973:A:G	acceptor_gain	1.0000
7:66944973:AAG:A	acceptor_gain	1.0000
7:66944974:A:G	acceptor_gain	1.0000
7:66944974:AG:A	acceptor_gain	1.0000
7:66944975:G:GT	acceptor_gain	1.0000
7:66944975:GG:G	acceptor_gain	1.0000
7:66944975:GGA:G	acceptor_gain	1.0000
7:66944975:GGATT:G	acceptor_gain	1.0000

AlphaMissense

2070 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:66941941:A:C	S26R	1.000
7:66941943:C:A	S26R	1.000
7:66941943:C:G	S26R	1.000
7:66941947:A:C	S28R	1.000
7:66941949:C:A	S28R	1.000
7:66941949:C:G	S28R	1.000
7:66944979:T:A	W55R	1.000
7:66944979:T:C	W55R	1.000
7:66944981:G:C	W55C	1.000
7:66944981:G:T	W55C	1.000
7:66953254:T:A	L270H	1.000
7:66953254:T:C	L270P	1.000
7:66953265:A:C	S274R	1.000
7:66953267:T:A	S274R	1.000
7:66953267:T:G	S274R	1.000
7:66953275:T:C	L277P	1.000
7:66953284:T:A	M280K	1.000
7:66953284:T:G	M280R	1.000
7:66953290:T:A	I282K	1.000
7:66941932:T:C	F23L	0.999
7:66941934:C:A	F23L	0.999
7:66941934:C:G	F23L	0.999
7:66941957:C:A	A31D	0.999
7:66941960:T:A	I32K	0.999
7:66941960:T:G	I32R	0.999
7:66941977:G:C	G38R	0.999
7:66944984:T:A	N56K	0.999
7:66944984:T:G	N56K	0.999
7:66945018:T:A	C68S	0.999
7:66945018:T:C	C68R	0.999

dbSNP variants (sampled 300 via entrez): RS1000080678 (7:66948049 T>C), RS1000133027 (7:66947646 C>A), RS1000150065 (7:66949627 T>C,G), RS1000239817 (7:66954283 T>C), RS1000269355 (7:66929105 C>T), RS1000284885 (7:66954028 C>G), RS1000512260 (7:66927546 T>C), RS1000518839 (7:66953102 C>G,T), RS1000577303 (7:66928898 C>A,T), RS1000838010 (7:66923893 T>C,G), RS1000976118 (7:66952926 G>A), RS1001008624 (7:66927803 A>C,G), RS1001033716 (7:66951244 A>T), RS1001053943 (7:66936059 G>A), RS1001198401 (7:66951542 T>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
GCST001806_9	Corneal structure	3.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004345	corneal topography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	affects methylation, increases abundance, increases expression	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
Valproic Acid	affects cotreatment, increases expression	2
bisphenol A	affects cotreatment, increases methylation	1
methylparaben	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
cobaltous chloride	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Dimethyl Sulfoxide	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Nickel	increases expression	1
Smoke	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Acrylamide	decreases expression	1
tert-Butylhydroperoxide	decreases expression	1

Clinical trials (associated diseases)

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