TMEM79

Summary

TMEM79 (transmembrane protein 79, HGNC:28196) is a protein-coding gene on chromosome 1q22, encoding Transmembrane protein 79 (Q9BSE2). Contributes to the epidermal integrity and skin barrier function.

Enables identical protein binding activity. Predicted to be involved in several processes, including epithelial cell maturation; establishment of skin barrier; and positive regulation of epidermis development. Predicted to act upstream of or within cornification; cuticle development; and hair follicle morphogenesis. Predicted to be located in Golgi apparatus; lysosome; and membrane. Predicted to be active in lysosomal membrane and trans-Golgi network membrane.

Source: NCBI Gene 84283 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_032323

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28196
Approved symbol	TMEM79
Name	transmembrane protein 79
Location	1q22
Locus type	gene with protein product
Status	Approved
Aliases	MGC13102, FLJ16057, FLJ32254, MATT
Ensembl gene	ENSG00000163472
Ensembl biotype	protein_coding
OMIM	615531
Entrez	84283

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000295694, ENST00000357501, ENST00000405535, ENST00000456810, ENST00000463670, ENST00000485135, ENST00000495881, ENST00000905697, ENST00000913287, ENST00000913288

RefSeq mRNA: 1 — MANE Select: NM_032323 NM_032323

CCDS: CCDS1138

Canonical transcript exons

ENST00000405535 — 4 exons

Exon	Start	End
ENSE00002295642	156284325	156284406
ENSE00003562947	156291385	156292443
ENSE00003579128	156286260	156286473
ENSE00003895310	156285184	156285983

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 98.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.9686 / max 169.0769, expressed in 1311 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5711	2.9735	1261
5712	1.9950	260

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	98.81	gold quality
upper arm skin	UBERON:0004263	98.16	gold quality
gingival epithelium	UBERON:0001949	97.87	gold quality
gingiva	UBERON:0001828	97.41	gold quality
esophagus mucosa	UBERON:0002469	97.16	gold quality
skin of abdomen	UBERON:0001416	96.30	gold quality
skin of leg	UBERON:0001511	96.05	gold quality
zone of skin	UBERON:0000014	95.37	gold quality
esophagus squamous epithelium	UBERON:0006920	94.66	gold quality
oral cavity	UBERON:0000167	93.30	gold quality
mammalian vulva	UBERON:0000997	91.91	gold quality
upper leg skin	UBERON:0004262	91.88	gold quality
pharyngeal mucosa	UBERON:0000355	89.70	gold quality
vagina	UBERON:0000996	89.10	gold quality
prostate gland	UBERON:0002367	86.05	gold quality
esophagus	UBERON:0001043	85.42	gold quality
amniotic fluid	UBERON:0000173	85.07	gold quality
mouth mucosa	UBERON:0003729	84.35	gold quality
skin of hip	UBERON:0001554	83.61	gold quality
penis	UBERON:0000989	83.39	gold quality
granulocyte	CL:0000094	83.24	gold quality
minor salivary gland	UBERON:0001830	82.59	gold quality
nipple	UBERON:0002030	81.08	gold quality
ectocervix	UBERON:0012249	80.33	gold quality
body of tongue	UBERON:0011876	80.22	gold quality
nasal cavity epithelium	UBERON:0005384	80.15	silver quality
tonsil	UBERON:0002372	79.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.31	gold quality
palpebral conjunctiva	UBERON:0001812	79.23	gold quality
mucosa of transverse colon	UBERON:0004991	79.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting TMEM79, 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-8485	100.00	77.57	4731
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-548AU-3P	99.70	68.22	1373
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-3194-3P	98.83	66.22	1167
HSA-MIR-1537-5P	98.70	68.33	999
HSA-MIR-3187-5P	98.36	65.74	1776
HSA-MIR-1285-3P	97.72	67.02	1932
HSA-MIR-5189-5P	97.72	66.96	1814
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-5699-5P	97.36	67.03	1014
HSA-MIR-612	97.26	65.95	1597
HSA-MIR-6860	97.21	66.31	1656
HSA-MIR-874-5P	96.93	63.92	1014
HSA-MIR-3918	96.13	64.65	1300
HSA-MIR-4793-3P	94.87	65.85	896

Literature-anchored findings (GeneRIF, showing 4)

• Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects. (PMID:24084074)
• The study identified two proteins, TMEM79 and ACOXL, with potential to differentiate between benign and cancerous prostatic glands in tissue biopsies. (PMID:26237329)
• Overexpression of TMEM79 combined with SMG5 is related to prognosis, tumor immune infiltration and drug sensitivity in hepatocellular carcinoma. (PMID:37936239)
• TMEM79 Ameliorates Cerebral Ischemia/Reperfusion Injury Through Regulating Inflammation and Oxidative Stress via the Nrf2/NLRP3 Pathway. (PMID:38809063)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem79a	ENSDARG00000071250
danio_rerio	tmem79b	ENSDARG00000076861
mus_musculus	Tmem79	ENSMUSG00000001420
rattus_norvegicus	Tmem79	ENSRNOG00000019414

Protein

Protein identifiers

Transmembrane protein 79 — Q9BSE2 (reviewed: Q9BSE2)

Alternative names: Mattrin

All UniProt accessions (3): Q9BSE2, Q5SZW9, Q5SZX3

UniProt curated annotations — full annotation on UniProt →

Function. Contributes to the epidermal integrity and skin barrier function. Plays a role in the lamellar granule (LG) secretory system and in the stratum corneum (SC) epithelial cell formation.

Subcellular location. Lysosome. Golgi apparatus. trans-Golgi network. Membrane.

Tissue specificity. Expressed in the epidermis of the skin. Expressed in epithelial cells of the outermost layer of the stratum granulosum (SG) and hair follicles (at protein level).

Disease relevance. Defects in TMEM79 may be associated with susceptibility to atopic dermatitis. Atopic dermatitis is a complex, inflammatory disease with multiple alleles at several loci thought to be involved in the pathogenesis. It commonly begins in infancy or early childhood and is characterized by a chronic relapsing form of skin inflammation, a disturbance of epidermal barrier function that culminates in dry skin, and IgE-mediated sensitization to food and environmental allergens. It is manifested by lichenification, excoriation, and crusting, mainly on the flexural surfaces of the elbow and knee.

RefSeq proteins (1): NP_115699* (*=MANE)

Domains & families (InterPro)

UniProt features (14 total): topological domain 6, transmembrane region 5, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BSE2-F1	61.74	0.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 155 (showing top): GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, RNGTGGGC_UNKNOWN, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_EPIDERMIS_MORPHOGENESIS, GOBP_REGULATION_OF_EPIDERMIS_DEVELOPMENT, GOBP_EPITHELIAL_CELL_DEVELOPMENT, GOCC_VACUOLAR_MEMBRANE, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, CAGCTG_AP4_Q5, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, GOBP_ANATOMICAL_STRUCTURE_MATURATION, GOBP_EXOCYTOSIS, GOCC_TRANS_GOLGI_NETWORK

GO Biological Process (7): epithelial cell maturation (GO:0002070), hair follicle morphogenesis (GO:0031069), cuticle development (GO:0042335), regulated exocytosis (GO:0045055), positive regulation of epidermis development (GO:0045684), establishment of skin barrier (GO:0061436), cornification (GO:0070268)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (6): lysosomal membrane (GO:0005765), trans-Golgi network membrane (GO:0032588), cytoplasm (GO:0005737), lysosome (GO:0005764), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
epithelial cell development	1
cell maturation	1
hair follicle development	1
anatomical structure morphogenesis	1
hair cycle process	1
epidermis morphogenesis	1
multicellular organism development	1
anatomical structure development	1
exocytosis	1
epidermis development	1
regulation of epidermis development	1
positive regulation of developmental process	1
skin epidermis development	1
programmed cell death	1
keratinization	1
cornified envelope assembly	1
protein binding	1
binding	1
lysosome	1
lytic vacuole membrane	1
trans-Golgi network	1
organelle membrane	1
intracellular anatomical structure	1
lytic vacuole	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

718 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM79	FLG	P20930	542
TMEM79	PPL	O60437	538
TMEM79	SMG5	Q9UPR3	519
TMEM79	FLG2	Q5D862	506
TMEM79	IQUB	Q8NA54	492
TMEM79	FNDC4	Q9H6D8	457
TMEM79	SPINK5	Q9NQ38	445
TMEM79	TTLL1	O95922	433
TMEM79	NINJ2	Q9NZG7	430
TMEM79	CRABP2	P29373	422
TMEM79	CDSN	Q15517	400
TMEM79	ACER1	Q8TDN7	399
TMEM79	PRDM8	Q9NQV8	398
TMEM79	EVPL	Q92817	375
TMEM79	FN3K	Q9H479	366

IntAct

174 interactions, top by confidence:

A	B	Type	Score
TMEM79	SFTPC	psi-mi:“MI:0915”(physical association)	0.900
SFTPC	TMEM79	psi-mi:“MI:0915”(physical association)	0.900
TMEM79	TEX264	psi-mi:“MI:0915”(physical association)	0.790
TEX264	TMEM79	psi-mi:“MI:0915”(physical association)	0.790
RNF8	TMEM79	psi-mi:“MI:0915”(physical association)	0.780
TMEM79	SEC22A	psi-mi:“MI:0915”(physical association)	0.780
TMEM79	RNF8	psi-mi:“MI:0915”(physical association)	0.780
SEC22A	TMEM79	psi-mi:“MI:0915”(physical association)	0.780

BioGRID (91): TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Two-hybrid), TMEM79 (Affinity Capture-MS)

ESM2 similar proteins: A1L3I3, A2A699, A2AWH2, A4IHZ3, A6NKQ9, A6QNY1, A8MVW0, B4R1D8, B6VH76, B6VH77, B6VH79, D3YY23, O00220, O43278, O55034, O75074, O88204, O95502, P08751, P21563, P22618, P48778, Q04756, Q3U2C5, Q3U4N7, Q496H8, Q4R6Y5, Q4TUC0, Q5HZW5, Q6QNF4, Q7TPG6, Q7TQH7, Q7Z4F1, Q86T13, Q86VZ4, Q8BY98, Q8C2B3, Q8C4W3, Q8CB67, Q8IXA5

Diamond homologs: Q3T1H8, Q5E9U3, Q9BSE2, Q9D709

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

625 predictions. Top by Δscore:

Variant	Effect	Δscore
1:156285106:A:T	donor_gain	1.0000
1:156286474:G:C	donor_loss	1.0000
1:156286474:G:GG	donor_gain	1.0000
1:156286475:T:G	donor_loss	1.0000
1:156291383:A:AG	acceptor_gain	1.0000
1:156291383:AGGCT:A	acceptor_gain	1.0000
1:156291384:G:GG	acceptor_gain	1.0000
1:156291384:GGCT:G	acceptor_gain	1.0000
1:156291384:GGCTG:G	acceptor_gain	1.0000
1:156285873:AC:A	acceptor_gain	0.9900
1:156285873:ACG:A	acceptor_gain	0.9900
1:156285873:ACGG:A	acceptor_gain	0.9900
1:156285874:C:CA	acceptor_gain	0.9900
1:156285874:C:G	acceptor_gain	0.9900
1:156285875:G:A	acceptor_gain	0.9900
1:156286014:G:T	donor_gain	0.9900
1:156286304:C:A	acceptor_gain	0.9900
1:156286469:TCCCG:T	donor_gain	0.9900
1:156286471:CCG:C	donor_gain	0.9900
1:156286472:CG:C	donor_gain	0.9900
1:156286473:GG:G	donor_gain	0.9900
1:156291380:CATA:C	acceptor_loss	0.9900
1:156291381:ATAG:A	acceptor_gain	0.9900
1:156291382:T:G	acceptor_gain	0.9900
1:156291382:TA:T	acceptor_loss	0.9900
1:156291383:AG:A	acceptor_gain	0.9900
1:156291383:AGG:A	acceptor_loss	0.9900
1:156291384:G:A	acceptor_gain	0.9900
1:156291384:G:GA	acceptor_loss	0.9900
1:156291384:GGC:G	acceptor_gain	0.9900

AlphaMissense

2496 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:156285983:G:A	G253R	0.996
1:156285983:G:C	G253R	0.996
1:156286393:C:A	N297K	0.996
1:156286393:C:G	N297K	0.996
1:156286460:T:C	F320L	0.996
1:156286462:T:A	F320L	0.996
1:156286462:T:G	F320L	0.996
1:156291481:C:A	N356K	0.996
1:156291481:C:G	N356K	0.996
1:156291456:C:G	P348R	0.995
1:156285963:C:A	A246D	0.994
1:156291395:T:A	W328R	0.994
1:156291395:T:C	W328R	0.994
1:156291441:G:A	G343D	0.994
1:156285950:T:C	C242R	0.993
1:156285972:C:G	P249R	0.993
1:156285983:G:T	G253W	0.993
1:156286395:T:C	L298P	0.993
1:156286461:T:C	F320S	0.993
1:156291447:C:A	T345K	0.993
1:156291456:C:A	P348Q	0.993
1:156286260:G:A	G253E	0.992
1:156286361:T:C	S287P	0.992
1:156286464:C:A	A321D	0.992
1:156286362:C:G	S287W	0.991
1:156291435:G:A	G341D	0.991
1:156285953:G:A	G243R	0.990
1:156285953:G:C	G243R	0.990
1:156285972:C:A	P249H	0.990
1:156286449:T:C	L316P	0.990

dbSNP variants (sampled 300 via entrez): RS1000242419 (1:156291240 A>G), RS1000528571 (1:156285065 G>C), RS1000665367 (1:156291779 C>T), RS1001247941 (1:156289471 G>C), RS1001476609 (1:156290275 CTCTTCT>C,CTCT), RS1001550071 (1:156292248 G>A), RS1001943946 (1:156283264 C>T), RS1002147218 (1:156292524 C>T), RS1002363419 (1:156288139 C>T), RS1002477958 (1:156288419 T>A), RS1002658503 (1:156288411 C>T), RS1002842704 (1:156281932 G>A), RS1002994760 (1:156282417 C>A), RS1003584904 (1:156281028 T>A), RS1003662414 (1:156286799 T>C,G)

Disease associations

OMIM: gene MIM:615531 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000582_7	Mean corpuscular hemoglobin concentration	3.000000e-09
GCST002390_1	Glycated hemoglobin levels	1.000000e-23
GCST005145_5	Glycated hemoglobin levels	1.000000e-07
GCST007953_1	Glycated hemoglobin levels	3.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004509	hemoglobin measurement
EFO:0004528	mean corpuscular hemoglobin concentration
EFO:0004541	HbA1c measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Calcitriol	increases expression, affects cotreatment	3
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
Acetaminophen	decreases expression, increases expression	2
Arsenic	increases expression, decreases expression, increases abundance, affects cotreatment	2
Cadmium Chloride	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
sodium arsenate	decreases expression, increases abundance	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	increases reaction, affects binding	1
pinostrobin	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
(+)-JQ1 compound	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	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases expression	1
Cisplatin	increases expression	1
Estradiol	decreases expression, affects cotreatment	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Hydrogen Peroxide	affects expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Mustard Gas	increases expression	1

Clinical trials (associated diseases)

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