POM121L2

Summary

POM121L2 (POM121 transmembrane nucleoporin like 2, HGNC:13973) is a protein-coding gene on chromosome 6p22.1, encoding POM121-like protein 2 (Q96KW2).

Predicted to enable nuclear localization sequence binding activity. Predicted to be a structural constituent of nuclear pore. Predicted to be involved in RNA export from nucleus and protein import into nucleus. Predicted to be part of nuclear pore.

Source: NCBI Gene 94026 — RefSeq curated summary.

At a glance

• GWAS associations: 33
• Clinical variants (ClinVar): 146 total
• MANE Select transcript: NM_033482

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13973
Approved symbol	POM121L2
Name	POM121 transmembrane nucleoporin like 2
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Aliases	POM121-L
Ensembl gene	ENSG00000158553
Ensembl biotype	protein_coding
Entrez	94026

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000429945, ENST00000444565

RefSeq mRNA: 1 — MANE Select: NM_033482 NM_033482

CCDS: CCDS59497

Canonical transcript exons

ENST00000444565 — 1 exons

Exon	Start	End
ENSE00001711609	27308377	27312273

Expression profiles

Bgee: expression breadth broad, 17 present calls, max score 77.04.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0451 / max 53.2280, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72366	0.0419	3
72367	0.0032	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 10	UBERON:0013541	77.04	gold quality
buccal mucosa cell	CL:0002336	70.81	gold quality
endometrium epithelium	UBERON:0004811	69.73	gold quality
left testis	UBERON:0004533	67.17	gold quality
frontal pole	UBERON:0002795	67.12	gold quality
right testis	UBERON:0004534	66.56	gold quality
middle frontal gyrus	UBERON:0002702	66.45	gold quality
paraflocculus	UBERON:0005351	66.35	gold quality
testis	UBERON:0000473	65.50	gold quality
pancreatic ductal cell	CL:0002079	64.08	silver quality
triceps brachii	UBERON:0001509	62.80	gold quality
gluteal muscle	UBERON:0002000	60.46	gold quality
tibialis anterior	UBERON:0001385	60.08	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	58.77	gold quality
cerebellar vermis	UBERON:0004720	57.62	gold quality
skin of hip	UBERON:0001554	57.11	gold quality
lateral nuclear group of thalamus	UBERON:0002736	56.23	gold quality
cranial nerve II	UBERON:0000941	56.03	silver quality
deltoid	UBERON:0001476	56.01	silver quality
quadriceps femoris	UBERON:0001377	55.63	gold quality
myocardium	UBERON:0002349	54.59	gold quality
substantia nigra pars reticulata	UBERON:0001966	54.58	gold quality
ileal mucosa	UBERON:0000331	54.42	gold quality
lateral globus pallidus	UBERON:0002476	54.22	gold quality
parotid gland	UBERON:0001831	54.13	gold quality
vastus lateralis	UBERON:0001379	53.97	gold quality
heart right ventricle	UBERON:0002080	53.69	gold quality
nasal cavity epithelium	UBERON:0005384	53.66	gold quality
upper leg skin	UBERON:0004262	53.62	gold quality
thymus	UBERON:0002370	53.27	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.46

Regulation

Is transcription factor: no

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pom121	ENSDARG00000055113
mus_musculus	Pom121l2	ENSMUSG00000016982
rattus_norvegicus	Pom121l2	ENSRNOG00000061510
drosophila_melanogaster	Nup153	FBGN0061200

Paralogs (6): NUP153 (ENSG00000124789), NUP214 (ENSG00000126883), NPAP1 (ENSG00000185823), POM121 (ENSG00000196313), POM121L12 (ENSG00000221900), POM121C (ENSG00000272391)

Protein

Protein identifiers

POM121-like protein 2 — Q96KW2 (reviewed: Q96KW2)

All UniProt accessions (2): Q96KW2, H7C418

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the POM121 family.

RefSeq proteins (1): NP_258443* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026054	Nucleoporin	Family

Pfam: PF15229

UniProt features (16 total): compositionally biased region 9, region of interest 6, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96KW2-F1	41.82	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_NUCLEAR_TRANSPORT, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_NUCLEAR_EXPORT, GOBP_RNA_LOCALIZATION, GOBP_PROTEIN_LOCALIZATION_TO_NUCLEUS, GOCC_NUCLEAR_ENVELOPE, GOCC_NUCLEAR_PORE, GOMF_SIGNAL_SEQUENCE_BINDING, GOMF_STRUCTURAL_CONSTITUENT_OF_NUCLEAR_PORE, GOMF_NUCLEAR_LOCALIZATION_SEQUENCE_BINDING, GSE13887_HEALTHY_VS_LUPUS_RESTING_CD4_TCELL_UP, GOMF_STRUCTURAL_MOLECULE_ACTIVITY

GO Biological Process (2): RNA export from nucleus (GO:0006405), protein import into nucleus (GO:0006606)

GO Molecular Function (2): nuclear localization sequence binding (GO:0008139), structural constituent of nuclear pore (GO:0017056)

GO Cellular Component (1): nuclear pore (GO:0005643)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA transport	1
nuclear export	1
intracellular protein transport	1
protein localization to nucleus	1
import into nucleus	1
establishment of protein localization to organelle	1
signal sequence receptor activity	1
structural molecule activity	1
nuclear pore	1
nucleocytoplasmic transport	1
nuclear envelope	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

252 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
POM121L2	NT5C2	P49902	618
POM121L2	PRSS16	Q9NQE7	614
POM121L2	ZNF184	Q99676	571
POM121L2	SLC17A1	Q14916	492
POM121L2	CNNM2	Q9H8M5	489
POM121L2	OR14J1	Q9UGF5	478
POM121L2	HMGN4	O00479	472
POM121L2	AS3MT	Q9HBK9	464
POM121L2	ZNF322	Q6U7Q0	445
POM121L2	SLC17A3	O00476	444
POM121L2	TENM4	Q6N022	440
POM121L2	ABT1	Q9ULW3	419
POM121L2	RNF113B	Q8IZP6	418
POM121L2	SPDYE1	Q8NFV5	412
POM121L2	SLC8A3	P57103	404

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A096MK47, A0A1D5RMD1, A2AQH4, A6NCI8, A8MUA0, A8MX80, B2RRE4, B7ZNG4, E9Q3S4, O15027, O94854, P70670, Q0GGX2, Q12802, Q12815, Q3URK3, Q3V0A6, Q5DTT3, Q5F2C3, Q5FW52, Q5H9F3, Q5SW25, Q5SWP3, Q5VV67, Q5VWP3, Q5VYM1, Q66HG9, Q69ZZ9, Q6NXZ1, Q6NZN1, Q6P1W5, Q711Q0, Q7TSG5, Q7Z434, Q86TB3, Q8K4E0, Q8N5Q1, Q8N9G6, Q8NFU7, Q8VCF0

Diamond homologs: A6NF01, A6NNC1, A8CG34, P52591, Q3SYA9, Q8K3Z9, Q96HA1, Q96KW2, Q6PJE2, Q8N7R1, Q5SW25, P10761, P21754, P23491, P42098, P48830, P48831, P48832, P48833, P53785, P53786, P79762, P97708

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	136
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

27 predictions. Top by Δscore:

Variant	Effect	Δscore
6:27311924:T:TA	donor_gain	0.6300
6:27309497:C:T	acceptor_gain	0.4800
6:27309497:C:CT	acceptor_gain	0.4700
6:27309135:A:T	acceptor_gain	0.4200
6:27311091:GCTT:G	donor_loss	0.3700
6:27311092:CTTA:C	donor_loss	0.3700
6:27311093:TT:T	donor_loss	0.3700
6:27311094:TA:T	donor_loss	0.3700
6:27311095:A:G	donor_loss	0.3700
6:27311096:CCT:C	donor_loss	0.3700
6:27309134:CAA:C	acceptor_gain	0.3300
6:27309361:T:G	acceptor_gain	0.3300
6:27311097:C:T	donor_loss	0.3200
6:27309360:T:TG	acceptor_gain	0.3000
6:27311088:GTTGC:G	donor_loss	0.3000
6:27311089:TTGCT:T	donor_loss	0.3000
6:27311090:TGCTT:T	donor_loss	0.3000
6:27310987:GTTTC:G	acceptor_gain	0.2600
6:27310988:TTTCT:T	acceptor_gain	0.2600
6:27309131:C:CT	acceptor_gain	0.2500
6:27309365:C:CT	acceptor_gain	0.2500
6:27309418:GCTCC:G	acceptor_gain	0.2400
6:27310989:TTCTG:T	acceptor_gain	0.2400
6:27311355:T:TA	donor_gain	0.2300
6:27311877:TTCCC:T	donor_gain	0.2300
6:27311098:T:C	donor_loss	0.2200
6:27311115:C:A	donor_loss	0.2000

AlphaMissense

6692 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:27311583:A:C	F196L	0.988
6:27311583:A:T	F196L	0.988
6:27311585:A:G	F196L	0.988
6:27311934:A:C	F79L	0.975
6:27311934:A:T	F79L	0.975
6:27311936:A:G	F79L	0.975
6:27309141:A:C	F1010L	0.962
6:27309141:A:T	F1010L	0.962
6:27309143:A:G	F1010L	0.962
6:27311823:G:C	S116R	0.950
6:27311823:G:T	S116R	0.950
6:27311825:T:G	S116R	0.950
6:27311584:A:G	F196S	0.946
6:27311547:A:C	F208L	0.938
6:27311547:A:T	F208L	0.938
6:27311549:A:G	F208L	0.938
6:27311584:A:C	F196C	0.930
6:27309498:A:C	F891L	0.928
6:27309498:A:T	F891L	0.928
6:27309500:A:G	F891L	0.928
6:27311397:G:C	S258R	0.928
6:27311397:G:T	S258R	0.928
6:27311399:T:G	S258R	0.928
6:27311882:A:G	W97R	0.925
6:27311882:A:T	W97R	0.925
6:27311880:C:A	W97C	0.923
6:27311880:C:G	W97C	0.923
6:27310440:G:C	F577L	0.906
6:27310440:G:T	F577L	0.906
6:27310442:A:G	F577L	0.906

dbSNP variants (sampled 300 via entrez): RS1001596414 (6:27310900 G>A,C), RS1001670603 (6:27308602 G>T), RS1001717866 (6:27309006 G>T), RS1002668382 (6:27310380 G>A,T), RS1002719195 (6:27310706 C>T), RS1003675657 (6:27312415 G>C), RS1003942952 (6:27311746 G>A), RS1004774335 (6:27309885 T>C,G), RS1004947174 (6:27310198 A>T), RS1005198334 (6:27312166 C>T), RS1006187371 (6:27311952 G>A,C,T), RS1006840468 (6:27313316 T>C), RS1007403011 (6:27308166 G>A), RS1009832020 (6:27309358 C>A,T), RS1010383981 (6:27309068 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

33 associations (top):

Study	Trait	p-value
GCST000433_1	Schizophrenia	1.000000e-08
GCST001851_14	Schizophrenia	4.000000e-07
GCST004110_13	Gait speed in old age	7.000000e-07
GCST004521_113	Autism spectrum disorder or schizophrenia	3.000000e-19
GCST004521_116	Autism spectrum disorder or schizophrenia	3.000000e-16
GCST004521_166	Autism spectrum disorder or schizophrenia	4.000000e-24
GCST004521_57	Autism spectrum disorder or schizophrenia	1.000000e-20
GCST004521_69	Autism spectrum disorder or schizophrenia	8.000000e-24
GCST004521_73	Autism spectrum disorder or schizophrenia	8.000000e-11
GCST005316_630	Intelligence (MTAG)	7.000000e-09
GCST006269_675	General cognitive ability	6.000000e-10
GCST006269_712	General cognitive ability	2.000000e-09
GCST006810_7	Self-reported risk-taking behaviour	4.000000e-10
GCST008152_65	Weight	2.000000e-06
GCST008162_33	Hip circumference	4.000000e-06
GCST008921_9	Asthma and major depressive disorder	3.000000e-08
GCST010002_50	Refractive error	4.000000e-34
GCST010083_13	Hemoglobin levels	2.000000e-11
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010142_74	Fish- and plant-related diet	9.000000e-09
GCST010142_82	Fish- and plant-related diet	3.000000e-08
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16
GCST012226_448	Waist circumference adjusted for body mass index	3.000000e-08
GCST012226_45	Waist circumference adjusted for body mass index	1.000000e-08

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0008579	risk-taking behaviour
EFO:0004338	body weight
EFO:0004509	hemoglobin measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0007789	BMI-adjusted waist circumference
EFO:0004736	aspartate aminotransferase measurement
EFO:0004533	alkaline phosphatase measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs41269255	Toxicity	3	opioids	Nausea;Vomiting

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs41269255	POM121L2	3	0.00	1	opioids

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, decreases methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression	1
Copper	affects cotreatment, decreases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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