PHAF1

Summary

PHAF1 (phagophore assembly factor 1, HGNC:29564) is a protein-coding gene on chromosome 16q22.1, encoding Phagosome assembly factor 1 (Q9BSU1). Plays a regulatory role in autophagic activity.

Predicted to be involved in Golgi to plasma membrane protein transport. Located in phagophore assembly site.

Source: NCBI Gene 80262 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 23 total
• MANE Select transcript: NM_025187

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29564
Approved symbol	PHAF1
Name	phagophore assembly factor 1
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Aliases	lin-10, FLJ12076, MYTHO
Ensembl gene	ENSG00000125149
Ensembl biotype	protein_coding
Entrez	80262

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000219139, ENST00000561683, ENST00000563853, ENST00000565900, ENST00000566026, ENST00000567162, ENST00000569277, ENST00000569600, ENST00000569626, ENST00000569683, ENST00000569914

RefSeq mRNA: 5 — MANE Select: NM_025187 NM_001320540, NM_001320541, NM_001320542, NM_001320543, NM_025187

CCDS: CCDS10828

Canonical transcript exons

ENST00000219139 — 16 exons

Exon	Start	End
ENSE00000688472	67145376	67145419
ENSE00000688473	67145570	67145628
ENSE00000688474	67146278	67146350
ENSE00000945610	67139984	67140117
ENSE00001206378	67147045	67148544
ENSE00001206381	67109941	67110239
ENSE00003474236	67140511	67140594
ENSE00003480964	67132817	67132911
ENSE00003581070	67131286	67131329
ENSE00003582868	67144834	67144877
ENSE00003587917	67120112	67120194
ENSE00003629442	67132446	67132525
ENSE00003632488	67134168	67134265
ENSE00003656776	67125959	67126042
ENSE00003657791	67134355	67134467
ENSE00003784543	67144294	67144376

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 92.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.2875 / max 125.4906, expressed in 1795 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154571	11.0954	1792
154572	0.8398	505
154570	0.3523	170

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	92.28	gold quality
oocyte	CL:0000023	91.55	gold quality
buccal mucosa cell	CL:0002336	90.71	gold quality
skin of leg	UBERON:0001511	90.22	gold quality
lower esophagus mucosa	UBERON:0035834	89.57	gold quality
skin of abdomen	UBERON:0001416	89.36	gold quality
secondary oocyte	CL:0000655	89.31	gold quality
monocyte	CL:0000576	89.14	gold quality
liver	UBERON:0002107	89.04	gold quality
leukocyte	CL:0000738	89.00	gold quality
gastrocnemius	UBERON:0001388	88.84	gold quality
muscle of leg	UBERON:0001383	88.31	gold quality
zone of skin	UBERON:0000014	88.30	gold quality
prefrontal cortex	UBERON:0000451	88.11	gold quality
granulocyte	CL:0000094	87.68	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	87.63	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.42	gold quality
upper arm skin	UBERON:0004263	87.26	gold quality
spinal cord	UBERON:0002240	86.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.44	gold quality
penis	UBERON:0000989	86.33	gold quality
pancreatic ductal cell	CL:0002079	86.31	silver quality
tibialis anterior	UBERON:0001385	86.12	silver quality
smooth muscle tissue	UBERON:0001135	85.75	gold quality
tendon of biceps brachii	UBERON:0008188	85.72	gold quality
cortical plate	UBERON:0005343	85.54	gold quality
stromal cell of endometrium	CL:0002255	85.27	gold quality
bone marrow cell	CL:0002092	85.13	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.05	gold quality
esophagus mucosa	UBERON:0002469	84.64	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting PHAF1, 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-1193	100.00	65.93	529
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815

Literature-anchored findings (GeneRIF, showing 1)

• C16ORF70/MYTHO promotes healthy aging in C.elegans and prevents cellular senescence in mammals. (PMID:38869949)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	phaf1	ENSDARG00000041560
mus_musculus	Phaf1	ENSMUSG00000031889
rattus_norvegicus	Phaf1	ENSRNOG00000014668
drosophila_melanogaster	CG7083	FBGN0035877

Paralogs (1): TBC1D32 (ENSG00000146350)

Protein

Protein identifiers

Phagosome assembly factor 1 — Q9BSU1 (reviewed: Q9BSU1)

All UniProt accessions (5): Q9BSU1, H3BRA5, H3BS58, H3BSG0, J3QRI8

UniProt curated annotations — full annotation on UniProt →

Function. Plays a regulatory role in autophagic activity. In complex with BCAS3, associates with the autophagosome formation site during both non-selective and selective autophagy.

Subunit / interactions. Interacts with BCAS3; the interaction is requrired for the association with the phagophore.

Subcellular location. Cytoplasm. Preautophagosomal structure.

Similarity. Belongs to the PHAF1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BSU1-1	1	yes
Q9BSU1-2	2

RefSeq proteins (5): NP_001307469, NP_001307470, NP_001307471, NP_001307472, NP_079463* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005373	PHAF1	Family
IPR039156	PHAF1/BROMI	Family

Pfam: PF03676

UniProt features (4 total): splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BSU1-F1	86.98	0.66

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 168 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, chr16q22, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, GOCC_TRANS_GOLGI_NETWORK, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, AAAGACA_MIR511, GOBP_GOLGI_TO_PLASMA_MEMBRANE_PROTEIN_TRANSPORT, GOCC_NEURON_PROJECTION, GOBP_LOCALIZATION_WITHIN_MEMBRANE, CAGCCTC_MIR4855P, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_PLASMA_MEMBRANE, TTTGCAC_MIR19A_MIR19B, GOCC_EXOCYTIC_VESICLE

GO Biological Process (1): Golgi to plasma membrane protein transport (GO:0043001)

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

GO Cellular Component (5): phagophore assembly site (GO:0000407), trans-Golgi network (GO:0005802), dendrite (GO:0030425), synaptic vesicle membrane (GO:0030672), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
Golgi to plasma membrane transport	1
protein transport	1
establishment of protein localization to plasma membrane	1
protein localization to plasma membrane	1
binding	1
cytoplasm	1
Golgi apparatus subcompartment	1
neuron projection	1
dendritic tree	1
synaptic vesicle	1
exocytic vesicle membrane	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

610 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PHAF1	BCAS3	Q9H6U6	614
PHAF1	ZNF311	Q5JNZ3	570
PHAF1	TEDC2	Q7L2K0	541
PHAF1	CCDC74B	Q96LY2	474
PHAF1	ARHGAP36	Q6ZRI8	447
PHAF1	WHAMM	Q8TF30	447
PHAF1	ZFYVE1	Q9HBF4	433
PHAF1	KCNK15	Q9H427	413
PHAF1	WDR45B	Q5MNZ6	411
PHAF1	DDRGK1	Q96HY6	397
PHAF1	PSME3IP1	Q9GZU8	394
PHAF1	ATG2A	Q2TAZ0	379
PHAF1	ZFAND2B	Q8WV99	372
PHAF1	MFSD2B	A6NFX1	370
PHAF1	LMBR1L	Q6UX01	367

IntAct

43 interactions, top by confidence:

A	B	Type	Score
PHAF1	TOLLIP	psi-mi:“MI:0915”(physical association)	0.670
ATXN3	PHAF1	psi-mi:“MI:0915”(physical association)	0.670
BCAS3	PHAF1	psi-mi:“MI:0915”(physical association)	0.660
WIPI2	BNIP3L	psi-mi:“MI:0914”(association)	0.640
PHAF1	BCAS3	psi-mi:“MI:0915”(physical association)	0.560
BCAS3	PHAF1	psi-mi:“MI:0915”(physical association)	0.560
TSHZ2	PHAF1	psi-mi:“MI:0915”(physical association)	0.560
CBFA2T2	PHAF1	psi-mi:“MI:0915”(physical association)	0.560
CCDC102B	PHAF1	psi-mi:“MI:0915”(physical association)	0.560
NPBWR2	PHAF1	psi-mi:“MI:0915”(physical association)	0.560
PRR5L	PHAF1	psi-mi:“MI:0915”(physical association)	0.560
PHAF1	TSHZ2	psi-mi:“MI:0915”(physical association)	0.560
MPPED1	PHAF1	psi-mi:“MI:0915”(physical association)	0.560
PHAF1	PSMG1	psi-mi:“MI:0914”(association)	0.530
WIPI2	PHAF1	psi-mi:“MI:0914”(association)	0.530
PHAF1	ATXN3	psi-mi:“MI:0915”(physical association)	0.400
C22orf15	GATB	psi-mi:“MI:0914”(association)	0.350
PHAF1	GAPDHS	psi-mi:“MI:0914”(association)	0.350
MAGEE1	FYN	psi-mi:“MI:0914”(association)	0.350
PHAF1	ARHGAP32	psi-mi:“MI:0914”(association)	0.350
CCDC102B	PHAF1	psi-mi:“MI:0915”(physical association)	0.000
TOLLIP	PHAF1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (102): C16orf70 (Two-hybrid), C16orf70 (Affinity Capture-MS), BCAS3 (Affinity Capture-MS), SERPINA3 (Affinity Capture-MS), NEFH (Affinity Capture-MS), NEFL (Affinity Capture-MS), CALML5 (Affinity Capture-MS), OCRL (Affinity Capture-MS), APPL1 (Affinity Capture-MS), SBSN (Affinity Capture-MS), CST6 (Affinity Capture-MS), NUP35 (Affinity Capture-MS), ANK3 (Affinity Capture-MS), MASTL (Affinity Capture-MS), SERPINB4 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IC37, A6QLC7, A7E2V1, B2RXC1, E9PY46, F6Y9J3, O02697, O08654, O75694, P37199, P48736, Q05B17, Q08D69, Q10569, Q10570, Q1LX49, Q1RLX4, Q1RMS6, Q24498, Q28DH9, Q3ZBT2, Q4U2V3, Q5F3K4, Q5R5N9, Q5U2X1, Q5U5D4, Q5ZI89, Q5ZL91, Q5ZLG9, Q6DDX8, Q6DK84, Q6P3K3, Q6PGF3, Q6PJI9, Q7TQK1, Q7Z392, Q802U2, Q8BH57, Q8BK06, Q8NFP9

Diamond homologs: O08654, P34692, Q922R1, Q9BSU1, Q9SD33, Q9VSH9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2303 predictions. Top by Δscore:

Variant	Effect	Δscore
16:67120106:TTTCA:T	acceptor_loss	1.0000
16:67120107:TTCA:T	acceptor_loss	1.0000
16:67120108:TCA:T	acceptor_loss	1.0000
16:67120109:CAGG:C	acceptor_loss	1.0000
16:67120110:A:AG	acceptor_gain	1.0000
16:67120110:A:T	acceptor_loss	1.0000
16:67120110:AG:A	acceptor_gain	1.0000
16:67120111:G:A	acceptor_loss	1.0000
16:67120111:G:GA	acceptor_gain	1.0000
16:67120111:GG:G	acceptor_gain	1.0000
16:67120111:GGA:G	acceptor_gain	1.0000
16:67120111:GGAAT:G	acceptor_gain	1.0000
16:67120191:ACAGG:A	donor_loss	1.0000
16:67120192:CAGG:C	donor_loss	1.0000
16:67120193:AGGTG:A	donor_loss	1.0000
16:67120194:GGTG:G	donor_loss	1.0000
16:67120195:G:GG	donor_gain	1.0000
16:67120196:T:G	donor_loss	1.0000
16:67125957:A:AG	acceptor_gain	1.0000
16:67125958:G:GG	acceptor_gain	1.0000
16:67132444:A:AG	acceptor_gain	1.0000
16:67132444:AGT:A	acceptor_gain	1.0000
16:67132445:G:GA	acceptor_gain	1.0000
16:67132445:GT:G	acceptor_gain	1.0000
16:67132445:GTG:G	acceptor_gain	1.0000
16:67132445:GTGGC:G	acceptor_gain	1.0000
16:67132524:AGGT:A	donor_loss	1.0000
16:67132525:GGTAA:G	donor_loss	1.0000
16:67132526:G:T	donor_loss	1.0000
16:67132527:T:G	donor_loss	1.0000

AlphaMissense

2793 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:67110198:C:A	P8H	1.000
16:67110239:G:A	G22R	1.000
16:67110239:G:C	G22R	1.000
16:67125990:T:C	L60P	1.000
16:67126011:T:C	L67P	1.000
16:67126038:T:A	L76H	1.000
16:67126038:T:C	L76P	1.000
16:67131320:T:C	L89S	1.000
16:67131325:T:C	Y91H	1.000
16:67132457:T:C	F96S	1.000
16:67132504:T:C	F112L	1.000
16:67132505:T:C	F112S	1.000
16:67132506:T:A	F112L	1.000
16:67132506:T:G	F112L	1.000
16:67132507:G:C	G113R	1.000
16:67132508:G:A	G113D	1.000
16:67132516:C:G	H116D	1.000
16:67132523:G:A	G118E	1.000
16:67132847:T:C	L129P	1.000
16:67132852:T:A	F131I	1.000
16:67132852:T:C	F131L	1.000
16:67132852:T:G	F131V	1.000
16:67132853:T:C	F131S	1.000
16:67132853:T:G	F131C	1.000
16:67132854:C:A	F131L	1.000
16:67132854:C:G	F131L	1.000
16:67132858:G:A	G133R	1.000
16:67132858:G:C	G133R	1.000
16:67132859:G:A	G133E	1.000
16:67132859:G:T	G133V	1.000

dbSNP variants (sampled 300 via entrez): RS1000009000 (16:67144934 T>C), RS1000016733 (16:67143471 T>C), RS1000235212 (16:67137808 C>T), RS1000357581 (16:67108909 A>G,T), RS1000369818 (16:67115923 C>A,T), RS1000396348 (16:67117691 C>T), RS1000531733 (16:67148098 A>G), RS1000759272 (16:67115501 C>G), RS1000812249 (16:67113981 G>A), RS1000920355 (16:67131189 T>TG), RS1000959659 (16:67108702 CT>C), RS1000963083 (16:67148559 T>A), RS1001130076 (16:67128652 C>T), RS1001255414 (16:67129466 G>A), RS1001330086 (16:67122212 T>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases mutagenesis, affects methylation	3
Cyclosporine	decreases expression	2
FR900359	decreases phosphorylation	1
trichostatin A	affects expression	1
benzo(e)pyrene	decreases methylation	1
epigallocatechin gallate	decreases expression	1
abrine	decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Fulvestrant	increases methylation	1
Leflunomide	decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Methapyrilene	decreases methylation	1
8-Bromo Cyclic Adenosine Monophosphate	decreases expression	1
Aflatoxin B1	decreases expression	1

Clinical trials (associated diseases)

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