CHMP4A

Summary

CHMP4A (charged multivesicular body protein 4A, HGNC:20274) is a protein-coding gene on chromosome 14q12, encoding Charged multivesicular body protein 4a (Q9BY43). Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs.

CHMP4A belongs to the chromatin-modifying protein/charged multivesicular body protein (CHMP) family. These proteins are components of ESCRT-III (endosomal sorting complex required for transport III), a complex involved in degradation of surface receptor proteins and formation of endocytic multivesicular bodies (MVBs). Some CHMPs have both nuclear and cytoplasmic/vesicular distributions, and one such CHMP, CHMP1A (MIM 164010), is required for both MVB formation and regulation of cell cycle progression (Tsang et al., 2006 [PubMed 16730941]).

Source: NCBI Gene 29082 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_014169

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20274
Approved symbol	CHMP4A
Name	charged multivesicular body protein 4A
Location	14q12
Locus type	gene with protein product
Status	Approved
Aliases	HSPC134, VPS32A, hSnf7-1, Snf7-1
Ensembl gene	ENSG00000254505
Ensembl biotype	protein_coding
OMIM	610051
Entrez	29082

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 5 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000347519, ENST00000524955, ENST00000527154, ENST00000530996, ENST00000531158, ENST00000533011, ENST00000533523, ENST00000534106, ENST00000542700, ENST00000552620, ENST00000889869, ENST00000921166

RefSeq mRNA: 1 — MANE Select: NM_014169 NM_014169

CCDS: CCDS9619

Canonical transcript exons

ENST00000347519 — 6 exons

Exon	Start	End
ENSE00001336881	24213409	24213488
ENSE00001492841	24209615	24209935
ENSE00003723636	24211415	24211592
ENSE00003728638	24210654	24210768
ENSE00003738282	24211680	24211829
ENSE00003783993	24210348	24210483

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 97.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.7105 / max 315.9716, expressed in 1814 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
142550	24.1618	1810
142551	1.5487	1096

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
popliteal artery	UBERON:0002250	97.77	gold quality
tibial artery	UBERON:0007610	97.77	gold quality
substantia nigra	UBERON:0002038	97.62	gold quality
granulocyte	CL:0000094	97.60	gold quality
monocyte	CL:0000576	97.60	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.60	gold quality
lower esophagus	UBERON:0013473	97.59	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.55	gold quality
leukocyte	CL:0000738	97.53	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.38	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.34	gold quality
mucosa of transverse colon	UBERON:0004991	97.32	gold quality
left coronary artery	UBERON:0001626	97.29	gold quality
amygdala	UBERON:0001876	97.26	gold quality
skin of abdomen	UBERON:0001416	97.14	gold quality
temporal lobe	UBERON:0001871	97.12	gold quality
lymph node	UBERON:0000029	97.03	gold quality
putamen	UBERON:0001874	97.03	gold quality
zone of skin	UBERON:0000014	96.97	gold quality
skin of leg	UBERON:0001511	96.91	gold quality
hypothalamus	UBERON:0001898	96.90	gold quality
spleen	UBERON:0002106	96.90	gold quality
right coronary artery	UBERON:0001625	96.85	gold quality
rectum	UBERON:0001052	96.83	gold quality
nucleus accumbens	UBERON:0001882	96.82	gold quality
prostate gland	UBERON:0002367	96.77	gold quality
colon	UBERON:0001155	96.76	gold quality
tibial nerve	UBERON:0001323	96.76	gold quality
Ammon’s horn	UBERON:0001954	96.73	gold quality
esophagus	UBERON:0001043	96.72	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.34
E-GEOD-110499	no	263.37

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TBP, ZNF143, ZNF236, ZNF699

miRNA regulators (miRDB)

18 targeting CHMP4A, 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-96-5P	99.95	72.80	2140
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-34B-5P	99.78	67.56	1175
HSA-MIR-449C-5P	99.78	67.63	1168
HSA-MIR-2682-5P	99.73	67.38	1055
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-6868-3P	98.63	69.64	2259
HSA-MIR-1237-3P	98.55	67.65	1423
HSA-MIR-1248	98.47	67.54	1314
HSA-MIR-3137	97.26	66.78	761
HSA-MIR-197-5P	97.23	68.10	596
HSA-MIR-6816-3P	95.05	66.08	459

Literature-anchored findings (GeneRIF, showing 9)

• hSnf7-1 binds to itself, membranes, and the AAA+ ATPase SKD1 (PMID:15632132)
• Cycles between a default ‘closed’ state and an activated ‘open’ state under control of sequences at their C-terminus and associated factors. (PMID:17547705)
• Study demonstrates that CHMP4A and CHMP4B proteins form novel membrane-attached filaments that can promote or stabilize negative curvature and outward budding. (PMID:18209100)
• The Bro1 domain of ALIX binds specifically to C-terminal residues of the human CHMP4A. (PMID:18511562)
• our results show that CHMP4A significantly enhances the stability and transcriptional activity of HIF-1alpha both under normoxic and hypoxic conditions (PMID:20888838)
• hSnf7-1 and hSnf7-2 are preferentially associated with CHMP2A and CHMP2B, respectively, and regulate the turnover of distinct transmembrane cargos such as neurotransmitter receptors in human neurons. (PMID:21975012)
• CC2D1A interaction with CHMP4B/4A blocks HIV-1 budding. (PMID:22258254)
• Chmp4, through Alix, recruits the human parainfluenza virus type 1 - C proteins to a common site on intracellular membranes and facilitates budding. (PMID:23527201)
• Roles of ESCRT Proteins ALIX and CHMP4A and Their Interplay with Interferon-Stimulated Gene 15 during Tick-Borne Flavivirus Infection. (PMID:34851141)

Cross-species orthologs

0 orthologs

Paralogs (5): CHMP5 (ENSG00000086065), CHMP4B (ENSG00000101421), CHMP7 (ENSG00000147457), CHMP4C (ENSG00000164695), CHMP4BP1 (ENSG00000258469)

Protein

Protein identifiers

Charged multivesicular body protein 4a — Q9BY43 (reviewed: Q9BY43)

Alternative names: Chromatin-modifying protein 4a, SNF7 homolog associated with Alix-2, SNF7-1, Vacuolar protein sorting-associated protein 32-1

All UniProt accessions (5): E9PQ80, E9PQI5, Q9BY43, H0YI89, H0YIN6

UniProt curated annotations — full annotation on UniProt →

Function. Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. When overexpressed, membrane-assembled circular arrays of CHMP4A filaments can promote or stabilize negative curvature and outward budding. Via its interaction with PDCD6IP involved in HIV-1 p6- and p9-dependent virus release. CHMP4A/B/C are required for the exosomal release of SDCBP, CD63 and syndecan.

Subunit / interactions. Probable core component of the endosomal sorting required for transport complex III (ESCRT-III). ESCRT-III components are thought to multimerize to form a flat lattice on the perimeter membrane of the endosome. Several assembly forms of ESCRT-III may exist that interact and act sequentially. Self-associates; overexpression leads to the assembly of filaments that curve and associate to create circular rings. Interacts with CHMP2A. Interacts with CHMP3; the interaction requires the release of CHMP4A autoinhibition. Interacts with CHMP4B. Interacts with CHMP4C. Interacts with CHMP6. Interacts with VPS4A. Interacts with PDCD6IP; the interaction is direct.

Subcellular location. Cytoplasmic vesicle membrane. Late endosome membrane.

Tissue specificity. Widely expressed. Expressed at higher level in heart, kidney, liver and skeletal muscle. Also expressed in brain, placenta, lung and pancreas.

Domain organisation. The acidic C-terminus and the basic N-termminus are thought to render the protein in a closed, soluble and inactive conformation through an autoinhibitory intramolecular interaction. The open and active conformation, which enables membrane binding and oligomerization, is achieved by interaction with other cellular binding partners, probably including other ESCRT components.

Similarity. Belongs to the SNF7 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BY43-1	1	yes
Q9BY43-2	2

RefSeq proteins (1): NP_054888* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005024	Snf7_fam	Family

Pfam: PF03357

UniProt features (20 total): region of interest 5, mutagenesis site 5, sequence conflict 3, coiled-coil region 2, chain 1, sequence variant 1, helix 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
3C3O	X-RAY DIFFRACTION	2.15
5MK1	X-RAY DIFFRACTION	2.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BY43-F1	79.98	0.45

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 (1): 196

Mutagenesis-validated functional residues (5):

Position	Phenotype
182–222	membrane association; releases autoinhibition.
209	reduces interaction with pdcd6ip.
214	abolishes interaction with pdcd6ip.
217	abolishes interaction with pdcd6ip.
220	abolishes interaction with pdcd6ip.

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-162588	Budding and maturation of HIV virion
R-HSA-1632852	Macroautophagy
R-HSA-5620971	Pyroptosis
R-HSA-917729	Endosomal Sorting Complex Required For Transport (ESCRT)
R-HSA-9610379	HCMV Late Events
R-HSA-9615710	Late endosomal microautophagy
R-HSA-9668328	Sealing of the nuclear envelope (NE) by ESCRT-III
R-HSA-9679504	Translation of Replicase and Assembly of the Replication Transcription Complex
R-HSA-9694676	Translation of Replicase and Assembly of the Replication Transcription Complex

MSigDB gene sets: 235 (showing top): GOBP_MITOTIC_CYTOKINESIS, REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT, GOBP_CHROMOSOME_ORGANIZATION, GOBP_NUCLEAR_MEMBRANE_REASSEMBLY, GOBP_LYSOSOMAL_TRANSPORT, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_ENDOSOME_ORGANIZATION, GOBP_VACUOLE_ORGANIZATION, GOBP_MEMBRANE_BIOGENESIS, GOCC_VACUOLAR_MEMBRANE, GOBP_VESICLE_ORGANIZATION, GOBP_CHROMOSOME_LOCALIZATION, GOZGIT_ESR1_TARGETS_DN, GOBP_ENDOSOME_TO_LYSOSOME_TRANSPORT, GOBP_MEMBRANE_FUSION

GO Biological Process (27): plasma membrane repair (GO:0001778), post-translational protein targeting to endoplasmic reticulum membrane (GO:0006620), vesicle budding from membrane (GO:0006900), autophagy (GO:0006914), nucleus organization (GO:0006997), mitotic metaphase chromosome alignment (GO:0007080), membrane invagination (GO:0010324), protein transport (GO:0015031), macroautophagy (GO:0016236), nuclear membrane reassembly (GO:0031468), late endosome to vacuole transport via multivesicular body sorting pathway (GO:0032511), multivesicular body assembly (GO:0036258), viral budding via host ESCRT complex (GO:0039702), ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162), viral budding from plasma membrane (GO:0046761), nervous system process (GO:0050877), protein polymerization (GO:0051258), vesicle fusion with vacuole (GO:0051469), multivesicular body-lysosome fusion (GO:0061763), midbody abscission (GO:0061952), multivesicular body sorting pathway (GO:0071985), membrane fission (GO:0090148), plasma membrane tubulation (GO:0097320), autophagosome maturation (GO:0097352), regulation of mitotic spindle assembly (GO:1901673), late endosome to lysosome transport (GO:1902774), vacuolar transport (GO:0007034)

GO Molecular Function (5): lipid binding (GO:0008289), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), ATPase binding (GO:0051117), protein binding (GO:0005515)

GO Cellular Component (21): autophagosome membrane (GO:0000421), kinetochore (GO:0000776), ESCRT III complex (GO:0000815), nucleus (GO:0005634), nuclear pore (GO:0005643), cytoplasm (GO:0005737), lysosomal membrane (GO:0005765), multivesicular body (GO:0005771), kinetochore microtubule (GO:0005828), cytosol (GO:0005829), plasma membrane (GO:0005886), cytoplasmic side of plasma membrane (GO:0009898), membrane coat (GO:0030117), midbody (GO:0030496), multivesicular body membrane (GO:0032585), amphisome membrane (GO:1904930), endosome (GO:0005768), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410), late endosome membrane (GO:0031902)

Reactome top-level categories

Rollup of top-8 pathways:

Category	Pathways
Autophagy	2
Late Phase of HIV Life Cycle	1
Regulated Necrosis	1
Membrane Trafficking	1
HCMV Infection	1
Nuclear Envelope (NE) Reassembly	1
SARS-CoV-1 Infection	1
Early SARS-CoV-2 Infection Events	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
membrane organization	3
cytoplasm	3
viral budding	2
vesicle fusion	2
binding	2
membrane protein complex	2
cytoplasmic vesicle	2
plasma membrane organization	1
wound healing	1
protein targeting to membrane	1
protein targeting to ER	1
vesicle organization	1
vesicle-mediated transport	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
organelle organization	1
mitotic sister chromatid segregation	1
mitotic cell cycle	1
metaphase chromosome alignment	1
mitotic cell cycle process	1
transport	1
intracellular protein localization	1
establishment of protein localization	1
autophagosome assembly	1
autophagy	1
membrane assembly	1
nuclear membrane organization	1
endosome transport via multivesicular body sorting pathway	1
late endosome to vacuole transport	1
multivesicular body organization	1
organelle assembly	1
ubiquitin-dependent protein catabolic process	1
protein catabolic process in the vacuole	1
multivesicular body sorting pathway	1
non-lytic viral release	1
system process	1
protein-containing complex assembly	1
vacuole fusion	1

Protein interactions and networks

STRING

544 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHMP4A	CHMP3	Q9Y3E7	999
CHMP4A	A0A140T963	A0A140T963	999
CHMP4A	CHMP2A	O43633	998
CHMP4A	PDCD6IP	Q8WUM4	996
CHMP4A	CHMP6	Q96FZ7	982
CHMP4A	CHMP1A	Q9HD42	960
CHMP4A	VPS4B	O75351	941
CHMP4A	VPS4A	Q9UN37	937
CHMP4A	CHMP2B	Q9UQN3	922
CHMP4A	TSG101	Q99816	919
CHMP4A	IST1	P53990	860
CHMP4A	CEP55	Q53EZ4	846
CHMP4A	PDCD6	O75340	843
CHMP4A	CC2D1A	Q6P1N0	833
CHMP4A	CDCA8	Q53HL2	816

IntAct

77 interactions, top by confidence:

A	B	Type	Score
SYT17	CHMP4A	psi-mi:“MI:0915”(physical association)	0.800
CHMP4A	SYT17	psi-mi:“MI:0915”(physical association)	0.800
CHMP4A	PDCD6IP	psi-mi:“MI:0407”(direct interaction)	0.680
PDCD6IP	CHMP4A	psi-mi:“MI:0407”(direct interaction)	0.680
CDCA3	CTDSPL	psi-mi:“MI:0914”(association)	0.670
CHMP4A	STAMBP	psi-mi:“MI:0915”(physical association)	0.550
STAMBP	CHMP4A	psi-mi:“MI:0915”(physical association)	0.550
ARL6IP6	YKT6	psi-mi:“MI:0914”(association)	0.530
VAX2	CHMP4A	psi-mi:“MI:0914”(association)	0.530
FYTTD1	UBA6	psi-mi:“MI:0914”(association)	0.530
SOX2	PDLIM1	psi-mi:“MI:0914”(association)	0.530
FSD1	UBFD1	psi-mi:“MI:0914”(association)	0.530
TAS2R41	YKT6	psi-mi:“MI:0914”(association)	0.530
FOXR2	NME2P1	psi-mi:“MI:0914”(association)	0.530
OR2K2	NME2P1	psi-mi:“MI:0914”(association)	0.530
RDH12	NME2P1	psi-mi:“MI:0914”(association)	0.530
VTA1	CHMP2A	psi-mi:“MI:0914”(association)	0.530
DAXX	TNRC18	psi-mi:“MI:0914”(association)	0.530
CHMP4A	USP54	psi-mi:“MI:0407”(direct interaction)	0.440
BROX	CHMP4A	psi-mi:“MI:0915”(physical association)	0.400
CHMP4B	CHMP4A	psi-mi:“MI:0915”(physical association)	0.370
CHMP5	CHMP4A	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (99): SYT17 (Two-hybrid), SYT17 (Two-hybrid), CHMP4A (Co-fractionation), CHMP4A (Co-fractionation), CHMP4A (Co-fractionation), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS), CHMP4A (Affinity Capture-MS)

ESM2 similar proteins: A2VDY3, O14177, O43633, O74422, P0C0A3, P0C149, P0CR54, P0CR55, P36108, P59074, Q4R574, Q503V0, Q54JK4, Q569C1, Q58CS7, Q5ABD0, Q5B5E0, Q5BKM3, Q5R861, Q5RAU5, Q5ZHN1, Q5ZL55, Q6BSH2, Q6CBS3, Q6DFS6, Q6GMA4, Q6GNN8, Q6IP52, Q6NRM7, Q6NU11, Q6NY88, Q753W3, Q7ZW25, Q86H98, Q871Y8, Q8CGS4, Q8GXN6, Q8T0Q4, Q96CF2, Q96FZ7

Diamond homologs: A2VDY3, O82197, P0C149, P0CR54, P0CR55, P39929, P59074, Q569C1, Q5ABD0, Q5B5E0, Q5XGW6, Q5ZHP5, Q6BSH2, Q6CBS3, Q6CJL0, Q6FW96, Q6GL11, Q6GNN8, Q6IQ73, Q753W3, Q7ZVC4, Q86H98, Q871Y8, Q8T0Q4, Q96CF2, Q9BY43, Q9D7F7, Q9D8B3, Q9H444, Q9P7F7, Q9SZE4, Q54KZ4, Q7T0X5, Q86K93, Q9VVI9, Q5R861, Q96FZ7, O74422, P0C0A3, Q54JK4

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
CHMP4A	“form complex”	ESCRT-III	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 85 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Budding and maturation of HIV virion	8	59.3×	1e-10
Endosomal Sorting Complex Required For Transport (ESCRT)	7	46.9×	1e-08
Macroautophagy	5	10.5×	4e-03
HCMV Late Events	5	8.9×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
viral budding via host ESCRT complex	7	77.0×	6e-10
nuclear membrane reassembly	5	67.9×	4e-07
multivesicular body sorting pathway	6	66.0×	4e-08
midbody abscission	6	60.2×	5e-08
multivesicular body assembly	8	57.7×	4e-10
ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	6	44.7×	2e-07
plasma membrane repair	5	39.8×	5e-06
nucleus organization	5	38.5×	5e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1255 predictions. Top by Δscore:

Variant	Effect	Δscore
14:24209955:C:CT	acceptor_gain	1.0000
14:24209955:C:T	acceptor_gain	1.0000
14:24209956:A:T	acceptor_gain	1.0000
14:24210343:CATA:C	donor_loss	1.0000
14:24210344:ATACC:A	donor_loss	1.0000
14:24210345:TACCT:T	donor_loss	1.0000
14:24210346:A:C	donor_loss	1.0000
14:24210347:C:CT	donor_loss	1.0000
14:24210347:CCTGG:C	donor_gain	1.0000
14:24210407:T:TA	donor_gain	1.0000
14:24210479:TCATC:T	acceptor_gain	1.0000
14:24210480:CATC:C	acceptor_gain	1.0000
14:24210480:CATCC:C	acceptor_gain	1.0000
14:24210481:ATC:A	acceptor_gain	1.0000
14:24210482:TC:T	acceptor_gain	1.0000
14:24210482:TCCTG:T	acceptor_loss	1.0000
14:24210483:CC:C	acceptor_gain	1.0000
14:24210484:C:A	acceptor_loss	1.0000
14:24210484:C:CC	acceptor_gain	1.0000
14:24210484:C:T	acceptor_gain	1.0000
14:24210488:A:AC	acceptor_gain	1.0000
14:24210488:A:C	acceptor_gain	1.0000
14:24210764:TGTCC:T	acceptor_gain	1.0000
14:24210767:CC:C	acceptor_gain	1.0000
14:24210767:CCCT:C	acceptor_loss	1.0000
14:24210768:CC:C	acceptor_gain	1.0000
14:24210768:CCTGA:C	acceptor_loss	1.0000
14:24210769:CTGAG:C	acceptor_loss	1.0000
14:24211413:A:AC	donor_gain	1.0000
14:24211414:C:CC	donor_gain	1.0000

AlphaMissense

1462 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:24211500:C:G	A92P	0.996
14:24211709:G:T	A51D	0.996
14:24211488:C:G	A96P	0.994
14:24211505:C:G	R90P	0.993
14:24211581:C:G	A65P	0.992
14:24210695:C:G	A145P	0.991
14:24211589:G:T	A62D	0.991
14:24211547:A:G	L76P	0.989
14:24211784:A:G	L26P	0.987
14:24211446:C:G	A110P	0.986
14:24211710:C:G	A51P	0.986
14:24211763:A:G	L33P	0.986
14:24211517:A:G	L86P	0.984
14:24211567:C:A	K69N	0.984
14:24211567:C:G	K69N	0.984
14:24211751:T:G	Q37P	0.984
14:24210745:A:G	L128P	0.983
14:24211577:A:G	L66S	0.983
14:24210703:A:C	I142S	0.980
14:24210703:A:G	I142T	0.980
14:24211449:C:G	A109P	0.979
14:24211466:A:G	L103P	0.978
14:24211718:A:G	L48P	0.978
14:24210464:A:G	L165P	0.977
14:24211586:A:G	L63P	0.977
14:24211508:T:G	Q89P	0.976
14:24211448:G:T	A109D	0.975
14:24211574:C:G	R67P	0.975
14:24210691:A:T	I146N	0.973
14:24211476:C:G	A100P	0.973

dbSNP variants (sampled 300 via entrez): RS1000169072 (14:24213821 G>A,T), RS1000982856 (14:24212741 A>T), RS1001062731 (14:24212107 T>C,G), RS1001386748 (14:24212196 C>T), RS1003833710 (14:24210136 G>T), RS1004509944 (14:24213214 G>T), RS1004684247 (14:24211940 A>G), RS1004755206 (14:24213468 C>G,T), RS1005354008 (14:24215212 A>G), RS1007420207 (14:24211375 C>T), RS1007849983 (14:24209882 A>G), RS1008016238 (14:24212665 C>T), RS1008379549 (14:24212385 G>A), RS1008530576 (14:24213044 C>T), RS1009620625 (14:24213343 G>A,T)

Disease associations

OMIM: gene MIM:610051 | 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

35 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, increases expression	2
bisphenol S	increases expression, affects cotreatment	2
Valproic Acid	affects expression, increases expression	2
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
cobaltous chloride	decreases expression	1
beta-methylcholine	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
azoxystrobin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
pyrachlostrobin	decreases expression	1
LDN 193189	increases expression, affects cotreatment	1
picoxystrobin	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Antimycin A	decreases expression	1
Atrazine	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Furaldehyde	affects localization, decreases expression, affects cotreatment	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Piroxicam	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Ribonucleotides	affects binding	1
Rotenone	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1ND	Abcam HeLa CHMP4A KO	Cancer cell line	Female

Clinical trials (associated diseases)

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