AVL9

Summary

AVL9 (AVL9 cell migration associated, HGNC:28994) is a protein-coding gene on chromosome 7p14.3, encoding Late secretory pathway protein AVL9 homolog (Q8NBF6). Functions in cell migration.

Involved in cell migration. Located in recycling endosome.

Source: NCBI Gene 23080 — RefSeq curated summary.

At a glance

• GWAS associations: 25
• Clinical variants (ClinVar): 104 total — 1 pathogenic
• MANE Select transcript: NM_015060

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28994
Approved symbol	AVL9
Name	AVL9 cell migration associated
Location	7p14.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000105778
Ensembl biotype	protein_coding
OMIM	612927
Entrez	23080

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 16 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000318709, ENST00000409301, ENST00000446718, ENST00000459629, ENST00000467779, ENST00000470500, ENST00000485228, ENST00000497020, ENST00000884406, ENST00000884407, ENST00000884408, ENST00000884409, ENST00000884410, ENST00000884411, ENST00000884412, ENST00000884413, ENST00000884414, ENST00000928171, ENST00000928172, ENST00000948734, ENST00000948735

RefSeq mRNA: 2 — MANE Select: NM_015060 NM_001410870, NM_015060

CCDS: CCDS34613, CCDS94078

Canonical transcript exons

ENST00000318709 — 16 exons

Exon	Start	End
ENSE00000675185	32548847	32548918
ENSE00000675188	32558559	32558628
ENSE00000675189	32558929	32559464
ENSE00000832274	32552229	32552295
ENSE00000832275	32553727	32553767
ENSE00000832276	32570020	32570154
ENSE00000832277	32573199	32573418
ENSE00001017122	32554558	32554596
ENSE00001278338	32580219	32580272
ENSE00001278348	32575955	32576072
ENSE00001278353	32544694	32544779
ENSE00001278362	32543141	32543261
ENSE00001823943	32583792	32588726
ENSE00001944463	32495489	32495802
ENSE00003492243	32580802	32580890
ENSE00003595749	32551334	32551423

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 93.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.2946 / max 169.4031, expressed in 1816 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
78052	25.0298	1816
78051	0.2648	101

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
choroid plexus epithelium	UBERON:0003911	93.69	gold quality
endothelial cell	CL:0000115	92.96	silver quality
Brodmann (1909) area 23	UBERON:0013554	92.23	gold quality
rectum	UBERON:0001052	92.18	gold quality
adrenal tissue	UBERON:0018303	92.06	gold quality
middle temporal gyrus	UBERON:0002771	91.36	gold quality
colonic mucosa	UBERON:0000317	90.80	gold quality
jejunal mucosa	UBERON:0000399	90.73	gold quality
buccal mucosa cell	CL:0002336	90.41	gold quality
mucosa of sigmoid colon	UBERON:0004993	90.26	gold quality
cortical plate	UBERON:0005343	90.17	gold quality
epithelium of nasopharynx	UBERON:0001951	90.01	gold quality
orbitofrontal cortex	UBERON:0004167	89.80	gold quality
lower esophagus mucosa	UBERON:0035834	89.80	gold quality
corpus epididymis	UBERON:0004359	89.65	gold quality
visceral pleura	UBERON:0002401	89.33	gold quality
germinal epithelium of ovary	UBERON:0001304	89.06	gold quality
islet of Langerhans	UBERON:0000006	89.03	gold quality
palpebral conjunctiva	UBERON:0001812	88.95	gold quality
pleura	UBERON:0000977	88.37	gold quality
parietal pleura	UBERON:0002400	88.35	gold quality
blood	UBERON:0000178	88.09	gold quality
bone marrow cell	CL:0002092	88.00	gold quality
pigmented layer of retina	UBERON:0001782	87.81	gold quality
Brodmann (1909) area 46	UBERON:0006483	87.71	gold quality
ganglionic eminence	UBERON:0004023	87.70	gold quality
ileal mucosa	UBERON:0000331	87.66	gold quality
superior frontal gyrus	UBERON:0002661	87.43	gold quality
duodenum	UBERON:0002114	87.05	gold quality
entorhinal cortex	UBERON:0002728	86.95	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.13
E-MTAB-7381	no	318.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

281 targeting AVL9, 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-6867-5P	100.00	82.21	3464
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-607	99.97	73.62	5593

Literature-anchored findings (GeneRIF, showing 2)

• Clinical significance and functions of miR-203a-3p/AVL9 axis in human non-small-cell lung cancer. (PMID:32678693)
• hsa_circ_0058357 acts as a ceRNA to promote nonsmall cell lung cancer progression via the hsamiR243p/AVL9 axis. (PMID:33880595)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	avl9	ENSDARG00000055538
mus_musculus	Avl9	ENSMUSG00000029787
rattus_norvegicus	Avl9	ENSRNOG00000013314
drosophila_melanogaster	CG11178	FBGN0030499
caenorhabditis_elegans		WBGENE00020822

Protein

Protein identifiers

Late secretory pathway protein AVL9 homolog — Q8NBF6 (reviewed: Q8NBF6)

All UniProt accessions (3): Q8NBF6, B8ZZW5, H7C0I1

UniProt curated annotations — full annotation on UniProt →

Function. Functions in cell migration.

Subcellular location. Recycling endosome. Membrane.

Similarity. Belongs to the AVL9 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NBF6-1	1	yes
Q8NBF6-2	2

RefSeq proteins (2): NP_001397799, NP_055875* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018307	ABL9/DENND6_dom	Domain
IPR037516	Tripartite_DENN	Domain
IPR051731	DENND11/AVL9_GEFs	Family

Pfam: PF09794

UniProt features (12 total): domain 3, region of interest 2, modified residue 2, chain 1, transmembrane region 1, splice variant 1, sequence variant 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NBF6-F1	73.73	0.56

Functional residue map

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

Post-translational modifications (2): 244, 588

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 187 (showing top): GGGACCA_MIR133A_MIR133B, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, MITSIADES_RESPONSE_TO_APLIDIN_DN, MODULE_195, DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN, MCBRYAN_PUBERTAL_BREAST_5_6WK_UP, MORF_EPHA7, CAIRO_HEPATOBLASTOMA_UP, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, CCAGGTT_MIR490, MODULE_277, MODULE_356, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN, CTGAGCC_MIR24

GO Biological Process (1): cell migration (GO:0016477)

GO Molecular Function (0):

GO Cellular Component (4): cytoplasm (GO:0005737), membrane (GO:0016020), recycling endosome (GO:0055037), endosome (GO:0005768)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cell motility	1
intracellular anatomical structure	1
endosome	1
endomembrane system	1
cytoplasmic vesicle	1

Protein interactions and networks

STRING

436 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
AVL9	DENND10	Q8TCE6	940
AVL9	DENND11	A4D1U4	938
AVL9	DENND6A	Q8IWF6	920
AVL9	DNM1L	O00429	716
AVL9	DENND5A	Q6IQ26	565
AVL9	RIC1	Q4ADV7	507
AVL9	RAB11A	P24410	472
AVL9	RAB33A	Q14088	442
AVL9	RAB30	Q15771	437
AVL9	ZNF688	P0C7X2	434
AVL9	MADD	Q8WXG6	431
AVL9	RAB33B	Q9H082	425
AVL9	RAB35	Q15286	413
AVL9	RAB18	Q9NP72	402
AVL9	DENND4B	O75064	401

IntAct

13 interactions, top by confidence:

A	B	Type	Score
KLC1	KIF5B	psi-mi:“MI:0914”(association)	0.730
POT1	TERF1	psi-mi:“MI:0914”(association)	0.530
TAFA4	NRP1	psi-mi:“MI:0914”(association)	0.530
Ppp2r1a	CCHCR1	psi-mi:“MI:0914”(association)	0.350
PARD6B	PARD3	psi-mi:“MI:0914”(association)	0.350
Cep72	TBC1D31	psi-mi:“MI:0914”(association)	0.350
PER3	CCDC88A	psi-mi:“MI:0914”(association)	0.350
MIDEAS	SEC16A	psi-mi:“MI:0914”(association)	0.350
NFKBIA	ATXN3	psi-mi:“MI:0914”(association)	0.350
HORMAD2	WASH3P	psi-mi:“MI:0914”(association)	0.350
DISC1	AVL9	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (30): AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Affinity Capture-MS), AVL9 (Synthetic Lethality), AVL9 (Affinity Capture-MS), AVL9 (Proximity Label-MS)

ESM2 similar proteins: A0JMF6, A2BGG1, A4D1P6, A6H8H2, A8E7C5, B2RYI0, E9PXF8, O15327, O70167, O70173, O95248, P97874, Q008S8, Q2HJE1, Q2I6J0, Q4R4D7, Q4R623, Q5PQS3, Q5R6T6, Q5R991, Q5RA60, Q5U581, Q5VZ89, Q5ZLD2, Q5ZLL7, Q63406, Q64096, Q6DIR8, Q6NTN5, Q6NU08, Q6P1Y8, Q6TEN6, Q6ZPE2, Q7TMQ7, Q7TPM9, Q7Z401, Q7ZXF1, Q803E0, Q80U56, Q86WG5

Diamond homologs: O13943, Q12500, Q5R991, Q80U56, Q8NBF6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	79
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
814947	GRCh37/hg19 7p15.3-14.3(chr7:23877135-33139446)x1	Pathogenic

SpliceAI

2706 predictions. Top by Δscore:

Variant	Effect	Δscore
7:32495801:AGGTG:A	donor_loss	1.0000
7:32495803:G:GA	donor_loss	1.0000
7:32543257:GGAAG:G	donor_gain	1.0000
7:32543258:GAAGG:G	donor_gain	1.0000
7:32543262:G:GA	donor_loss	1.0000
7:32548928:G:GT	donor_gain	1.0000
7:32551331:A:AG	acceptor_gain	1.0000
7:32551332:A:G	acceptor_gain	1.0000
7:32552228:GGA:G	acceptor_gain	1.0000
7:32552293:TTGG:T	donor_loss	1.0000
7:32552295:GGT:G	donor_loss	1.0000
7:32552296:GTAA:G	donor_loss	1.0000
7:32552297:TAAG:T	donor_loss	1.0000
7:32552298:AA:A	donor_loss	1.0000
7:32554626:G:GT	donor_gain	1.0000
7:32570011:A:AG	acceptor_gain	1.0000
7:32570012:A:G	acceptor_gain	1.0000
7:32570018:A:AG	acceptor_gain	1.0000
7:32570018:AG:A	acceptor_gain	1.0000
7:32570018:AGG:A	acceptor_gain	1.0000
7:32570019:G:GA	acceptor_loss	1.0000
7:32570019:G:GG	acceptor_gain	1.0000
7:32570019:GG:G	acceptor_gain	1.0000
7:32570019:GGG:G	acceptor_gain	1.0000
7:32570019:GGGAT:G	acceptor_gain	1.0000
7:32570041:AT:A	acceptor_gain	1.0000
7:32570042:T:G	acceptor_gain	1.0000
7:32570150:TGG:T	donor_gain	1.0000
7:32570152:G:GT	donor_gain	1.0000
7:32570152:G:T	donor_gain	1.0000

AlphaMissense

4242 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:32495779:T:C	F24L	1.000
7:32495780:T:C	F24S	1.000
7:32495781:T:A	F24L	1.000
7:32495781:T:G	F24L	1.000
7:32495785:C:G	H26D	1.000
7:32543207:T:A	W54R	1.000
7:32543207:T:C	W54R	1.000
7:32543229:C:A	A61D	1.000
7:32543237:G:C	D64H	1.000
7:32543241:G:A	G65D	1.000
7:32544763:G:C	R95P	1.000
7:32548878:G:C	R111T	1.000
7:32548878:G:T	R111I	1.000
7:32548879:A:C	R111S	1.000
7:32548879:A:T	R111S	1.000
7:32548887:T:A	V114D	1.000
7:32548891:G:C	Q115H	1.000
7:32548891:G:T	Q115H	1.000
7:32548894:A:C	K116N	1.000
7:32548894:A:T	K116N	1.000
7:32548895:A:C	S117R	1.000
7:32548897:T:A	S117R	1.000
7:32548897:T:G	S117R	1.000
7:32548899:T:A	V118D	1.000
7:32548905:T:A	V120D	1.000
7:32551362:T:C	L134P	1.000
7:32551382:T:G	Y141D	1.000
7:32551385:T:C	F142L	1.000
7:32551387:T:A	F142L	1.000
7:32551387:T:G	F142L	1.000

dbSNP variants (sampled 300 via entrez): RS1000035971 (7:32534793 T>A,C), RS1000046709 (7:32495555 G>A,T), RS1000063447 (7:32533450 C>T), RS1000096791 (7:32538064 T>G), RS1000102760 (7:32536089 G>T), RS1000120628 (7:32496910 A>G), RS1000149691 (7:32582859 A>AT), RS1000153451 (7:32584106 G>A), RS1000180295 (7:32540946 T>A,C,G), RS1000208841 (7:32586423 C>T), RS1000223640 (7:32557249 C>T), RS1000232789 (7:32516789 G>A), RS1000306447 (7:32507414 T>A), RS1000362454 (7:32515009 A>G), RS1000374867 (7:32554576 C>A,G,T)

Disease associations

OMIM: gene MIM:612927 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

25 associations (top):

Study	Trait	p-value
GCST004621_111	Red cell distribution width	7.000000e-33
GCST005316_1	Intelligence (MTAG)	1.000000e-08
GCST005951_156	Body mass index	3.000000e-08
GCST006804_159	Red cell distribution width	6.000000e-09
GCST006804_19	Red cell distribution width	2.000000e-62
GCST007044_17	Extremely high intelligence	5.000000e-08
GCST90002385_184	High light scatter reticulocyte count	3.000000e-12
GCST90002386_446	High light scatter reticulocyte percentage of red cells	1.000000e-14
GCST90002390_243	Mean corpuscular hemoglobin	5.000000e-16
GCST90002392_718	Mean corpuscular volume	9.000000e-15
GCST90002396_382	Mean reticulocyte volume	3.000000e-18
GCST90002404_284	Red cell distribution width	3.000000e-22
GCST90002405_225	Reticulocyte count	1.000000e-20
GCST90002406_244	Reticulocyte fraction of red cells	2.000000e-09
GCST90002406_245	Reticulocyte fraction of red cells	4.000000e-18
GCST90020025_1101	Waist-to-hip ratio adjusted for BMI	3.000000e-08
GCST90020025_1102	Waist-to-hip ratio adjusted for BMI	5.000000e-08
GCST90020025_1103	Waist-to-hip ratio adjusted for BMI	5.000000e-10
GCST90020026_551	Hip index	2.000000e-08
GCST90020026_552	Hip index	5.000000e-09
GCST90020026_553	Hip index	2.000000e-08
GCST90020027_1354	Waist-hip index	3.000000e-08
GCST90020027_1355	Waist-hip index	2.000000e-08
GCST90020027_1356	Waist-hip index	1.000000e-10
GCST90020028_159	Hip circumference adjusted for BMI	2.000000e-08

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0009188	Red cell distribution width
EFO:0004337	intelligence
EFO:0004340	body mass index
EFO:0007986	reticulocyte count
EFO:0004527	mean corpuscular hemoglobin
EFO:0010701	mean reticulocyte volume
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, decreases methylation	4
Cyclosporine	increases expression, increases methylation	3
Benzo(a)pyrene	decreases expression, affects methylation	2
Aflatoxin B1	decreases methylation, increases methylation	2
GSK-J4	increases expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
coumarin	affects phosphorylation	1
perfluorooctane sulfonic acid	increases expression	1
abrine	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Hydrogen Peroxide	increases expression	1
Ivermectin	decreases expression	1
Methapyrilene	increases methylation	1
Nickel	increases expression	1
Ozone	increases abundance, affects expression	1
Plant Extracts	affects cotreatment, increases expression	1
Selenium	decreases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Zinc	affects cotreatment, increases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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