TMEM167B

Summary

TMEM167B (transmembrane protein 167B, HGNC:30187) is a protein-coding gene on chromosome 1p13.3, encoding Protein kish-B (Q9NRX6). Involved in the early part of the secretory pathway.

Involved in constitutive secretory pathway. Located in Golgi apparatus.

Source: NCBI Gene 56900 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_020141

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30187
Approved symbol	TMEM167B
Name	transmembrane protein 167B
Location	1p13.3
Locus type	gene with protein product
Status	Approved
Aliases	AD-020, FLJ90710
Ensembl gene	ENSG00000215717
Ensembl biotype	protein_coding
Entrez	56900

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000338272, ENST00000473828, ENST00000479160, ENST00000651489, ENST00000873084, ENST00000946557

RefSeq mRNA: 2 — MANE Select: NM_020141 NM_001322248, NM_020141

CCDS: CCDS30789, CCDS91014

Canonical transcript exons

ENST00000338272 — 3 exons

Exon	Start	End
ENSE00001207374	109094417	109096934
ENSE00001906581	109090764	109090882
ENSE00003649627	109092890	109093021

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 98.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 38.0364 / max 481.5210, expressed in 1820 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4379	37.5535	1819
4380	0.4117	169
4378	0.0712	27

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	98.49	gold quality
cardiac muscle of right atrium	UBERON:0003379	98.04	gold quality
cartilage tissue	UBERON:0002418	96.62	gold quality
monocyte	CL:0000576	96.18	gold quality
corpus epididymis	UBERON:0004359	96.13	gold quality
islet of Langerhans	UBERON:0000006	96.11	gold quality
tibia	UBERON:0000979	96.02	gold quality
decidua	UBERON:0002450	96.01	gold quality
leukocyte	CL:0000738	95.97	gold quality
caput epididymis	UBERON:0004358	95.43	gold quality
ileal mucosa	UBERON:0000331	95.42	gold quality
cortical plate	UBERON:0005343	95.33	gold quality
left ventricle myocardium	UBERON:0006566	95.19	gold quality
pigmented layer of retina	UBERON:0001782	95.12	gold quality
tibialis anterior	UBERON:0001385	95.10	gold quality
nasal cavity epithelium	UBERON:0005384	95.06	gold quality
skin of hip	UBERON:0001554	95.04	gold quality
myocardium	UBERON:0002349	95.03	gold quality
amniotic fluid	UBERON:0000173	94.76	gold quality
vena cava	UBERON:0004087	94.72	gold quality
bone marrow	UBERON:0002371	94.71	gold quality
kidney epithelium	UBERON:0004819	94.66	gold quality
pericardium	UBERON:0002407	94.63	gold quality
deltoid	UBERON:0001476	94.55	gold quality
layer of synovial tissue	UBERON:0007616	94.18	gold quality
seminal vesicle	UBERON:0000998	94.15	gold quality
nasal cavity mucosa	UBERON:0001826	94.03	gold quality
placenta	UBERON:0001987	93.96	gold quality
postcentral gyrus	UBERON:0002581	93.92	gold quality
smooth muscle tissue	UBERON:0001135	93.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

148 targeting TMEM167B, 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-6873-3P	100.00	71.42	2626
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem167b	ENSDARG00000059400
rattus_norvegicus	Tmem167b-ps1	ENSRNOG00000000376
rattus_norvegicus	Tmem167b	ENSRNOG00000088396
caenorhabditis_elegans		WBGENE00303023

Paralogs (1): TMEM167A (ENSG00000174695)

Protein

Protein identifiers

Protein kish-B — Q9NRX6 (reviewed: Q9NRX6)

Alternative names: Transmembrane protein 167B

All UniProt accessions (2): Q9NRX6, A0A494C0V7

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the early part of the secretory pathway.

Subcellular location. Golgi apparatus membrane.

Similarity. Belongs to the KISH family.

RefSeq proteins (2): NP_001309177, NP_064526* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009653	Ksh1	Family
IPR042863	Kish-B	Family

Pfam: PF06842

UniProt features (5 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NRX6-F1	69.92	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 121 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, ZHAN_MULTIPLE_MYELOMA_PR_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EXOCYTOSIS, GOBP_SECRETION, GCM_NF2, ACEVEDO_LIVER_CANCER_UP, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, CAMPS_COLON_CANCER_COPY_NUMBER_DN, GCM_CSNK1A1, HORIUCHI_WTAP_TARGETS_UP, GCM_DENR, GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_UP

GO Biological Process (1): constitutive secretory pathway (GO:0045054)

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

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
exocytosis	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

362 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM167B	KRTAP12-4	P60329	583
TMEM167B	WDR47	O94967	507
TMEM167B	FNDC7	Q5VTL7	475
TMEM167B	CFAP276	Q5T5A4	462
TMEM167B	EEIG2	Q5T8I3	460
TMEM167B	AKNAD1	Q5T1N1	456
TMEM167B	UBL4B	Q8N7F7	448
TMEM167B	TRAPPC6B	Q86SZ2	437
TMEM167B	TAF13	Q15543	421
TMEM167B	TTC29	Q8NA56	420
TMEM167B	ZNF627	Q7L945	418
TMEM167B	SNX14	Q9Y5W7	406
TMEM167B	CST8	O60676	384
TMEM167B	COMMD10	Q9Y6G5	369
TMEM167B	HMSD	A8MTL9	360

IntAct

101 interactions, top by confidence:

A	B	Type	Score
TMEM167B	HSD17B13	psi-mi:“MI:0915”(physical association)	0.560
NRAC	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
MGST2	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
LSS	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
ZDHHC21	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
EBP	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
TM4SF19	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
TMEM167B	AGPAT3	psi-mi:“MI:0915”(physical association)	0.560
TMEM167B	PLLP	psi-mi:“MI:0915”(physical association)	0.560
SEC22B	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
APOL3	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
TMEM107	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
AQP6	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
SLC34A3	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
HSD17B13	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
ACKR2	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
CD47	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
CD300C	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
UNC50	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
MFSD14B	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
STX12	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
HSD17B11	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560
TAS2R19	TMEM167B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (41): TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid), TMEM167B (Two-hybrid)

ESM2 similar proteins: A0A318, A0A7H0DNB3, A2VDC5, A3PBJ1, A4ZUB9, B0BN70, B5G2S6, G2TRS3, O31867, O64834, P0CAM0, P0CAM1, P0CAM2, P0CAM3, P0CK27, P0CK28, P15900, P18034, P53089, Q09X34, Q0IIL4, Q148I3, Q28FL7, Q28GL2, Q3SZ97, Q54HH9, Q54J38, Q57788, Q58704, Q5BJC2, Q5RAL1, Q5RAU6, Q5RKS2, Q5WG37, Q5ZII6, Q65176, Q6AZW1, Q6DE23, Q70LB3, Q76TT7

Diamond homologs: A2VDC5, B5G2S6, G2TRS3, Q0IIL4, Q148I3, Q28FL7, Q28GL2, Q54HH9, Q5BJC2, Q5RAL1, Q5RAU6, Q5ZII6, Q6AZW1, Q6DE23, Q80X45, Q8TBQ9, Q8TGJ3, Q9CR64, Q9NRX6, Q9VWH8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

428 predictions. Top by Δscore:

Variant	Effect	Δscore
1:109090883:G:GA	donor_loss	0.9900
1:109090884:T:G	donor_loss	0.9900
1:109092955:A:T	donor_gain	0.9900
1:109093087:G:GT	donor_gain	0.9900
1:109090857:TCC:T	donor_gain	0.9800
1:109090878:GAACG:G	donor_gain	0.9800
1:109090883:G:GG	donor_gain	0.9800
1:109092888:A:AG	acceptor_gain	0.9800
1:109092889:G:GG	acceptor_gain	0.9800
1:109092889:GT:G	acceptor_gain	0.9800
1:109094416:GCC:G	acceptor_gain	0.9800
1:109093085:AGGG:A	donor_gain	0.9700
1:109094494:A:G	acceptor_gain	0.9700
1:109090885:GA:G	donor_loss	0.9600
1:109092997:G:GT	donor_gain	0.9600
1:109093084:TAGG:T	donor_gain	0.9600
1:109094415:A:AG	acceptor_gain	0.9600
1:109094416:G:GG	acceptor_gain	0.9600
1:109090790:G:GT	donor_gain	0.9500
1:109090790:G:T	donor_gain	0.9500
1:109093083:G:GG	donor_gain	0.9500
1:109093095:G:GG	donor_gain	0.9400
1:109094411:T:TA	acceptor_gain	0.9400
1:109090910:TGG:T	donor_gain	0.9300
1:109090911:GGG:G	donor_gain	0.9300
1:109093010:T:A	donor_gain	0.9300
1:109093082:A:AG	donor_gain	0.9300
1:109093094:A:AG	donor_gain	0.9300
1:109094493:A:AG	acceptor_gain	0.9300
1:109094493:AAAAT:A	acceptor_gain	0.9300

AlphaMissense

469 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:109092919:G:C	G14R	0.999
1:109094428:G:A	G52R	0.999
1:109094428:G:C	G52R	0.999
1:109094429:G:A	G52E	0.999
1:109092920:G:A	G14D	0.998
1:109092940:T:C	C21R	0.998
1:109094429:G:T	G52V	0.998
1:109094435:G:T	R54M	0.998
1:109092904:G:A	G9R	0.997
1:109092904:G:C	G9R	0.997
1:109092997:G:C	G40R	0.997
1:109093006:G:C	G43R	0.997
1:109093020:A:C	K47N	0.997
1:109093020:A:T	K47N	0.997
1:109094426:T:A	I51N	0.997
1:109092905:G:A	G9E	0.996
1:109092934:T:C	C19R	0.996
1:109092941:G:A	C21Y	0.996
1:109094461:T:C	C63R	0.996
1:109094462:G:A	C63Y	0.996
1:109092904:G:T	G9W	0.995
1:109092932:T:A	V18D	0.995
1:109092935:G:A	C19Y	0.995
1:109094419:G:C	A49P	0.995
1:109094453:C:A	A60E	0.995
1:109094463:T:G	C63W	0.995
1:109092926:T:A	L16H	0.994
1:109092926:T:C	L16P	0.994
1:109092936:C:G	C19W	0.994
1:109092997:G:T	G40C	0.994

dbSNP variants (sampled 300 via entrez): RS1000055214 (1:109091740 C>T), RS1000463595 (1:109092489 T>C), RS1000656111 (1:109093111 T>C), RS1000890721 (1:109090990 G>C), RS1000957868 (1:109093471 G>A), RS1001561758 (1:109093410 T>G), RS1001898485 (1:109088997 G>A,T), RS1002136070 (1:109093736 G>A), RS1002590719 (1:109095940 T>C), RS1002702798 (1:109090704 G>A), RS1002705432 (1:109095632 C>G), RS1002941038 (1:109090162 G>T), RS1003652527 (1:109089661 G>A), RS1004406252 (1:109095361 G>A), RS1004564125 (1:109095564 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

3 associations (top):

Study	Trait	p-value
GCST010243_123	Apolipoprotein B levels	3.000000e-11
GCST90011900_51	Serum alkaline phosphatase levels	1.000000e-12
GCST90013406_128	Liver enzyme levels (alkaline phosphatase)	3.000000e-24

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004615	apolipoprotein B measurement
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression	2
Cyclosporine	increases expression	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	increases expression, affects cotreatment	1
jinfukang	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Diuron	decreases expression	1
Doxorubicin	decreases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Urethane	increases expression	1
Valproic Acid	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Lactic Acid	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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