APOLTP

Summary

APOLTP (apolipoprotein lipid transfer particle homolog, HGNC:53879) is a protein-coding gene on chromosome 16p13.13, encoding Protein APOLTP (Q6ZTK2).

At a glance

• Clinical variants (ClinVar): 13 total
• GTEx eGene: eQTL in 38 tissues, sQTL in 7 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.75 (unconstrained)
• MANE Select transcript: NM_001370704

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53879
Approved symbol	APOLTP
Name	apolipoprotein lipid transfer particle homolog
Location	16p13.13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000188897
Ensembl biotype	protein_coding
Entrez	400499

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

MANE Select: ENST00000696174

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 2: 1, TSL 3: 3, TSL 5: 4

ENST00000696174, ENST00000595168, ENST00000595170, ENST00000596416, ENST00000598234, ENST00000599216, ENST00000600548, ENST00000600877, ENST00000612858

RefSeq mRNA: 2 — MANE Select: NM_001370704 NM_001370704, NM_001395505

CCDS: CCDS92107, CCDS92108

Canonical transcript exons

ENST00000696174 — 67 exons

Exon	Start	End
ENSE00002975720	11518900	11518970
ENSE00002984000	11425125	11425433
ENSE00003002119	11439489	11439581
ENSE00003005356	11383642	11383783
ENSE00003010379	11516142	11516307
ENSE00003014577	11523420	11523473
ENSE00003017568	11494575	11494760
ENSE00003017619	11384216	11384325
ENSE00003024151	11500804	11500969
ENSE00003030190	11396511	11396675
ENSE00003032672	11402037	11402158
ENSE00003047202	11393391	11393559
ENSE00003047471	11493644	11493796
ENSE00003048177	11440724	11440843
ENSE00003066781	11502077	11502180
ENSE00003073935	11411246	11411327
ENSE00003074010	11487262	11487386
ENSE00003092957	11440939	11441076
ENSE00003101144	11390279	11390463
ENSE00003108411	11383886	11384008
ENSE00003109041	11387111	11387295
ENSE00003109102	11372015	11372738
ENSE00003109264	11514359	11514539
ENSE00003110723	11515929	11516063
ENSE00003112935	11385211	11385416
ENSE00003115743	11392010	11392102
ENSE00003117386	11423179	11423256
ENSE00003123739	11407200	11407337
ENSE00003138122	11392317	11392501
ENSE00003146197	11491701	11491845
ENSE00003153306	11435662	11435879
ENSE00003153979	11417632	11417839
ENSE00003154015	11399472	11399600
ENSE00003180872	11390105	11390202
ENSE00003186235	11521952	11522112
ENSE00003189996	11508716	11508855
ENSE00003206319	11414342	11414508
ENSE00003206998	11424109	11424344
ENSE00003207734	11384888	11385065
ENSE00003208082	11391666	11391861
ENSE00003209345	11431036	11431229
ENSE00003464084	11478530	11478685
ENSE00003466458	11399702	11399815
ENSE00003470138	11459896	11460054
ENSE00003477111	11448919	11449107
ENSE00003478114	11401266	11401406
ENSE00003479141	11475624	11475715
ENSE00003481947	11476764	11476946
ENSE00003486476	11488709	11488867
ENSE00003494323	11477821	11478005
ENSE00003514146	11447934	11448073
ENSE00003520271	11456859	11457039
ENSE00003521984	11471654	11471817
ENSE00003539136	11469175	11469254
ENSE00003544395	11460477	11460610
ENSE00003558511	11484879	11485073
ENSE00003611313	11412841	11412953
ENSE00003622217	11404704	11404866
ENSE00003628407	11460964	11461119
ENSE00003637050	11446748	11446910
ENSE00003647619	11450609	11450820
ENSE00003655129	11446550	11446636
ENSE00003676388	11462117	11462303
ENSE00003689104	11469508	11469667
ENSE00003753352	11398348	11398509
ENSE00003966315	11423865	11424026
ENSE00004787452	11527109	11527247

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 90.89.

Highest expression (Bgee): nasal cavity epithelium, kidney epithelium, vena cava, blood, ventricle myocardium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

APOLTP is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 38 tissues and its splicing (sQTL) in 7 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 45 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Whole Blood	sqtl	5.3e-85	-1.26	16:11388371:C:G
Cells EBV-transformed lymphocytes	eqtl	9.7e-39	-0.99	16:11495905:A:C
Testis	sqtl	6.5e-32	-1.28	16:11388391:C:T
Lung	sqtl	2.8e-19	-0.83	16:11388041:A:G
Nerve Tibial	eqtl	3.5e-16	+0.46	16:11416772:A:G
Muscle Skeletal	eqtl	1.1e-15	+0.36	16:11489660:A:G
Skin Sun Exposed Lower leg	eqtl	1.8e-15	+0.24	16:11501111:T:TG
Skin Sun Exposed Lower leg	sqtl	3.0e-13	-0.67	16:11383900:C:T
Brain Cerebellar Hemisphere	eqtl	1.9e-12	+0.83	16:11401704:C:T
Brain Cerebellum	eqtl	9.4e-12	+0.81	16:11401704:C:T
Whole Blood	eqtl	1.1e-11	+0.21	16:11416772:A:G
Thyroid	eqtl	6.8e-11	+0.45	16:11416918:C:T
Testis	eqtl	6.2e-10	+0.27	16:11491188:T:C
Spleen	sqtl	9.4e-10	-1.20	16:11395117:A:T
Adipose Visceral Omentum	sqtl	9.8e-09	-0.58	16:11388391:C:T
Skin Not Sun Exposed Suprapubic	eqtl	1.3e-07	+0.20	16:11501655:C:T
Adipose Subcutaneous	eqtl	2.8e-07	-0.25	16:11548386:T:C
Brain Nucleus accumbens basal ganglia	eqtl	3.5e-07	+0.43	16:11527364:T:C
Pituitary	eqtl	3.5e-06	+0.42	16:11401704:C:T
Lung	eqtl	2.8e-05	+0.36	16:11416772:A:G

Top tissues by expression

showing 100 of 235 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
nasal cavity epithelium	UBERON:0005384	90.89	silver quality
kidney epithelium	UBERON:0004819	90.59	gold quality
vena cava	UBERON:0004087	90.44	silver quality
blood	UBERON:0000178	90.23	gold quality
left ventricle myocardium	UBERON:0006566	89.16	gold quality
epithelial cell of pancreas	CL:0000083	87.84	gold quality
lateral nuclear group of thalamus	UBERON:0002736	87.81	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	87.37	gold quality
cardiac muscle of right atrium	UBERON:0003379	87.06	gold quality
myocardium	UBERON:0002349	86.84	gold quality
parotid gland	UBERON:0001831	86.20	gold quality
subthalamic nucleus	UBERON:0001906	86.05	silver quality
pons	UBERON:0000988	85.98	silver quality
body of tongue	UBERON:0011876	85.93	silver quality
dorsal plus ventral thalamus	UBERON:0001897	85.08	silver quality
vastus lateralis	UBERON:0001379	84.24	gold quality
substantia nigra pars compacta	UBERON:0001965	83.75	silver quality
pericardium	UBERON:0002407	83.55	silver quality
inferior vagus X ganglion	UBERON:0005363	83.50	silver quality
cardia of stomach	UBERON:0001162	83.42	gold quality
trachea	UBERON:0003126	83.12	silver quality
pylorus	UBERON:0001166	82.81	silver quality
medulla oblongata	UBERON:0001896	82.81	silver quality
superior vestibular nucleus	UBERON:0007227	82.09	silver quality
saphenous vein	UBERON:0007318	82.04	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	81.85	gold quality
cerebellar vermis	UBERON:0004720	81.71	gold quality
spleen	UBERON:0002106	81.44	gold quality
biceps brachii	UBERON:0001507	81.09	gold quality
renal medulla	UBERON:0000362	80.52	gold quality
granulocyte	CL:0000094	79.82	gold quality
trigeminal ganglion	UBERON:0001675	79.58	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.51	gold quality
sperm	CL:0000019	79.31	silver quality
synovial joint	UBERON:0002217	78.12	silver quality
layer of synovial tissue	UBERON:0007616	77.75	gold quality
thymus	UBERON:0002370	77.65	silver quality
dorsal root ganglion	UBERON:0000044	77.38	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.21	gold quality
gingival epithelium	UBERON:0001949	76.89	gold quality
endothelial cell	CL:0000115	76.77	gold quality
skeletal muscle tissue	UBERON:0001134	75.76	gold quality
muscle tissue	UBERON:0002385	75.17	gold quality
pancreatic ductal cell	CL:0002079	74.84	silver quality
caecum	UBERON:0001153	74.56	gold quality
right lung	UBERON:0002167	74.39	gold quality
upper lobe of left lung	UBERON:0008952	73.49	gold quality
pigmented layer of retina	UBERON:0001782	73.44	gold quality
apex of heart	UBERON:0002098	73.32	gold quality
cartilage tissue	UBERON:0002418	73.05	silver quality
jejunum	UBERON:0002115	72.86	gold quality
skin of leg	UBERON:0001511	72.75	gold quality
penis	UBERON:0000989	72.64	gold quality
trabecular bone tissue	UBERON:0002483	72.59	silver quality
nasal cavity mucosa	UBERON:0001826	72.54	gold quality
bone marrow	UBERON:0002371	72.41	gold quality
superficial temporal artery	UBERON:0001614	72.40	gold quality
epithelium of mammary gland	UBERON:0003244	72.15	gold quality
oocyte	CL:0000023	72.14	gold quality
mammary duct	UBERON:0001765	72.03	gold quality
tibia	UBERON:0000979	72.00	silver quality
upper lobe of lung	UBERON:0008948	71.53	gold quality
vermiform appendix	UBERON:0001154	71.38	gold quality
decidua	UBERON:0002450	71.30	silver quality
metanephros	UBERON:0000081	71.23	gold quality
colonic mucosa	UBERON:0000317	71.16	silver quality
Brodmann (1909) area 23	UBERON:0013554	70.85	gold quality
deltoid	UBERON:0001476	70.81	gold quality
zone of skin	UBERON:0000014	70.64	gold quality
descending thoracic aorta	UBERON:0002345	70.64	gold quality
right uterine tube	UBERON:0001302	70.63	gold quality
secondary oocyte	CL:0000655	70.59	gold quality
mucosa of sigmoid colon	UBERON:0004993	70.49	silver quality
esophagus squamous epithelium	UBERON:0006920	70.30	gold quality
bronchus	UBERON:0002185	70.11	gold quality
Brodmann (1909) area 46	UBERON:0006483	69.69	silver quality
sural nerve	UBERON:0015488	69.68	gold quality
bronchial epithelial cell	CL:0002328	69.55	gold quality
left testis	UBERON:0004533	68.97	gold quality
superior frontal gyrus	UBERON:0002661	68.89	silver quality
skin of abdomen	UBERON:0001416	68.88	gold quality
right testis	UBERON:0004534	68.73	gold quality
left uterine tube	UBERON:0001303	68.68	gold quality
cortex of kidney	UBERON:0001225	68.46	gold quality
ascending aorta	UBERON:0001496	68.44	gold quality
thoracic aorta	UBERON:0001515	68.40	gold quality
seminal vesicle	UBERON:0000998	68.29	silver quality
testis	UBERON:0000473	68.25	gold quality
palpebral conjunctiva	UBERON:0001812	68.16	gold quality
medial globus pallidus	UBERON:0002477	68.09	silver quality
oral cavity	UBERON:0000167	67.88	gold quality
metanephros cortex	UBERON:0010533	67.67	gold quality
kidney	UBERON:0002113	67.50	gold quality
liver	UBERON:0002107	67.48	gold quality
myometrium	UBERON:0001296	67.40	gold quality
gastrocnemius	UBERON:0001388	67.14	gold quality
mammary gland	UBERON:0001911	67.14	gold quality
midbrain	UBERON:0001891	67.11	gold quality
thoracic mammary gland	UBERON:0005200	67.05	gold quality
jejunal mucosa	UBERON:0000399	66.88	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.39

Regulation

Is transcription factor: no

Functional genomics

gnomAD constraint: pLI 3.45e-72, LOEUF 1.75, missense Z -5.4 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000598234 — one region, missense o/e 1.27.

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkeyp-106c3.1	ENSDARG00000090623

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
RMI2	protein-coding	116028
LITAF	protein-coding	9516
MIR548H2	ncRNA	100313773
PRM1	protein-coding	5619
PRM2	protein-coding	5620
PRM3	protein-coding	58531
TNP2	protein-coding	7142
SOCS1	protein-coding	8651
TXNDC11	protein-coding	51061
SNN	protein-coding	8303
TXNDC11-AS1	ncRNA	127379753

Protein

Protein identifiers

Protein APOLTP — Q6ZTK2 (reviewed: Q6ZTK2)

Alternative names: Apolipoprotein lipid transfer particle homolog

All UniProt accessions (6): A0A8Q3SIG1, M0QZD8, M0R1J3, M0R2I5, M0R2X1, Q6ZTK2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

RefSeq proteins (2): NP_001357633, NP_001382434 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR048484	APOLTP_dom	Domain

Pfam: PF21013

UniProt features (29 total): glycosylation site 25, sequence variant 2, signal peptide 1, chain 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZTK2-F1	87.88	0.61

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (25)

Type	Positions
N-linked (glcnac…) asparagine	1694, 1704, 1743, 1891, 1905, 1962, 1987, 2104, 2135, 2154, 60, 2414, 2572, 2583, 2682, 2795, 3006, 3141, 466, 657, 820, 1112, 1136, 1276, 1472

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 0 (showing top):

GO Biological Process (1): lipid transport (GO:0006869)

GO Molecular Function (1): lipid carrier activity (GO:0005319)

GO top-level categories

3 GO namespaces:

Category	Terms
transport	1
lipid localization	1
molecular carrier activity	1

Protein interactions and networks

STRING

showing 15 of 568 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
APOLTP	NECAB2	Q7Z6G3	427
APOLTP	REM2	Q8IYK8	426
APOLTP	O15348	O15348	418
APOLTP	RCC1	P18754	356
APOLTP	TERT	O14746	335
APOLTP	THPO	P40225	334
APOLTP	ALDH18A1	P54886	331
APOLTP	CENPF	P49454	323
APOLTP	PTPRZ1	P23471	323
APOLTP	WDR46	O15213	322
APOLTP	EBNA1BP2	Q99848	322
APOLTP	GHSR	Q92847	321
APOLTP	NOC4L	Q9BVI4	313
APOLTP	CSPG4	Q6UVK1	311
APOLTP	PLA2G2E	Q9NZK7	309

Disease & clinical

Genetic variants

Variant evidence for APOLTP: 13 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	13
Benign	0

AlphaMissense

2,367 missense substitutions predicted likely pathogenic (of 21,352 scored), across 930 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
F3026	8	0.937	0.987
F3224	8	0.926	0.992
F3205	8	0.922	0.982
D175	8	0.897	0.957
F3051	8	0.855	0.977
D3045	8	0.822	0.914
D979	8	0.779	0.837
D593	8	0.769	0.873
C180	7	0.933	0.978
C200	7	0.933	0.977
C3215	7	0.932	0.978
C3252	7	0.930	0.968
F3216	7	0.923	0.972
F580	7	0.897	0.972
C370	7	0.893	0.956
N150	7	0.892	0.973
C241	7	0.891	0.939
C3228	7	0.890	0.939
C3131	7	0.887	0.954
D3151	7	0.875	0.912

Disease associations

OMIM: gene `` | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.