VMAC

Summary

VMAC (vimentin type intermediate filament associated coiled-coil protein, HGNC:33803) is a protein-coding gene on chromosome 19p13.3, encoding Vimentin-type intermediate filament-associated coiled-coil protein (Q2NL98).

Predicted to be located in cytoplasm. Predicted to be active in type III intermediate filament.

Source: NCBI Gene 400673 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_001017921

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33803
Approved symbol	VMAC
Name	vimentin type intermediate filament associated coiled-coil protein
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187650
Ensembl biotype	protein_coding
OMIM	617204
Entrez	400673

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000339485

RefSeq mRNA: 1 — MANE Select: NM_001017921 NM_001017921

CCDS: CCDS32881

Canonical transcript exons

ENST00000339485 — 2 exons

Exon	Start	End
ENSE00001382705	5908824	5910853
ENSE00002964559	5904872	5905081

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 82.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.9500 / max 137.5056, expressed in 1775 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173437	8.9500	1775

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.60	gold quality
granulocyte	CL:0000094	80.11	gold quality
fundus of stomach	UBERON:0001160	77.97	gold quality
body of stomach	UBERON:0001161	76.69	gold quality
monocyte	CL:0000576	76.60	gold quality
leukocyte	CL:0000738	76.51	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.98	silver quality
blood	UBERON:0000178	75.81	gold quality
prostate gland	UBERON:0002367	75.46	gold quality
right adrenal gland cortex	UBERON:0035827	75.35	gold quality
body of pancreas	UBERON:0001150	75.33	gold quality
stomach	UBERON:0000945	75.31	gold quality
right lobe of thyroid gland	UBERON:0001119	75.13	gold quality
right adrenal gland	UBERON:0001233	75.03	gold quality
left lobe of thyroid gland	UBERON:0001120	74.43	gold quality
left adrenal gland cortex	UBERON:0035825	74.18	gold quality
left adrenal gland	UBERON:0001234	74.16	gold quality
saliva-secreting gland	UBERON:0001044	74.14	gold quality
minor salivary gland	UBERON:0001830	74.10	gold quality
thyroid gland	UBERON:0002046	74.01	gold quality
small intestine Peyer’s patch	UBERON:0003454	73.87	gold quality
lower esophagus muscularis layer	UBERON:0035833	73.87	gold quality
lower esophagus	UBERON:0013473	73.84	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	73.71	gold quality
pituitary gland	UBERON:0000007	73.66	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	73.56	gold quality
stromal cell of endometrium	CL:0002255	73.54	gold quality
spleen	UBERON:0002106	73.53	gold quality
right ovary	UBERON:0002118	73.51	gold quality
small intestine	UBERON:0002108	73.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting VMAC, 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-3120-5P	100.00	65.56	965
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-302A-5P	99.39	68.21	1913
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-4662A-5P	98.48	67.18	1007
HSA-MIR-4433A-3P	97.75	62.82	1435
HSA-MIR-6773-5P	97.04	64.30	595
HSA-MIR-6724-5P	96.41	63.11	507
HSA-MIR-4522	95.76	66.23	742
HSA-MIR-4524B-3P	95.52	64.12	964
HSA-MIR-671-3P	92.07	62.01	40

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	VMAC	ENSDARG00000110997
danio_rerio	VMAC	ENSDARG00000115939
mus_musculus	Vmac	ENSMUSG00000054723
rattus_norvegicus	Vmac	ENSRNOG00000065863

Protein

Protein identifiers

Vimentin-type intermediate filament-associated coiled-coil protein — Q2NL98 (reviewed: Q2NL98)

All UniProt accessions (1): Q2NL98

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

RefSeq proteins (1): NP_001017921* (*=MANE)

Domains & families (InterPro)

UniProt features (5 total): compositionally biased region 2, chain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2NL98-F1	86.31	0.70

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 66 (showing top): TTTGTAG_MIR520D, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, chr19p13, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER, BARX1_TARGET_GENES, CEBPZ_TARGET_GENES, DIDO1_TARGET_GENES, GLI3_TARGET_GENES, HES4_TARGET_GENES, HMG20B_TARGET_GENES, HOXC13_TARGET_GENES, KLF7_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (2): cytoplasm (GO:0005737), type III intermediate filament (GO:0045098)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
intermediate filament	1

Protein interactions and networks

STRING

112 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VMAC	WDPCP	O95876	475
VMAC	CAMKK1	Q8N5S9	389
VMAC	ITGA10	O75578	367
VMAC	PRRG3	Q9BZD7	360
VMAC	CGA	P01215	358
VMAC	NICN1	Q9BSH3	348
VMAC	DTWD1	Q8N5C7	333
VMAC	PLPPR5	Q32ZL2	316
VMAC	TTC21A	Q8NDW8	274
VMAC	CDKN3	Q16667	265
VMAC	CENPE	Q02224	263
VMAC	RAB44	Q7Z6P3	258
VMAC	RASL11A	Q6T310	248
VMAC	ZDBF2	Q9HCK1	232
VMAC	RNF34	Q969K3	223

IntAct

67 interactions, top by confidence:

A	B	Type	Score
VMAC	BANP	psi-mi:“MI:0915”(physical association)	0.680
ZBTB25	VMAC	psi-mi:“MI:0915”(physical association)	0.560
VMAC	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
ZNF80	VMAC	psi-mi:“MI:0915”(physical association)	0.560
VMAC	ZNF326	psi-mi:“MI:0915”(physical association)	0.560
TFAP4	VMAC	psi-mi:“MI:0915”(physical association)	0.560
VMAC	LNX1	psi-mi:“MI:0915”(physical association)	0.560
VMAC	LMO3	psi-mi:“MI:0915”(physical association)	0.560
VMAC	SDK2	psi-mi:“MI:0915”(physical association)	0.560
LMO4	VMAC	psi-mi:“MI:0915”(physical association)	0.560
VMAC	SAXO4	psi-mi:“MI:0915”(physical association)	0.560
VMAC	SPG21	psi-mi:“MI:0915”(physical association)	0.560
LMO2	VMAC	psi-mi:“MI:0915”(physical association)	0.560
PSMA1	VMAC	psi-mi:“MI:0915”(physical association)	0.560
VMAC	NGLY1	psi-mi:“MI:0915”(physical association)	0.560
VMAC	KANK2	psi-mi:“MI:0915”(physical association)	0.560
SMR3A	VMAC	psi-mi:“MI:0914”(association)	0.530
ESR2	FBLL1	psi-mi:“MI:0914”(association)	0.460
VMAC	BANP	psi-mi:“MI:0915”(physical association)	0.400
VMAC	DLG4	psi-mi:“MI:0915”(physical association)	0.370
RPL22L1	FAAP100	psi-mi:“MI:0914”(association)	0.350
ORF24	MVK	psi-mi:“MI:0914”(association)	0.350
ZBTB25	VMAC	psi-mi:“MI:0915”(physical association)	0.000
BANP	VMAC	psi-mi:“MI:0915”(physical association)	0.000
SCNM1	VMAC	psi-mi:“MI:0915”(physical association)	0.000
ZNF80	VMAC	psi-mi:“MI:0915”(physical association)	0.000
ZNF326	VMAC	psi-mi:“MI:0915”(physical association)	0.000
TFAP4	VMAC	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (27): VMAC (Affinity Capture-MS), VMAC (Affinity Capture-MS), BANP (Affinity Capture-MS), BANP (Affinity Capture-MS), VMAC (Affinity Capture-MS), VMAC (Affinity Capture-MS), VMAC (Two-hybrid), VMAC (Two-hybrid), VMAC (Two-hybrid), VMAC (Two-hybrid), VMAC (Two-hybrid), VMAC (Two-hybrid), VMAC (Two-hybrid), VMAC (Two-hybrid), VMAC (Two-hybrid)

ESM2 similar proteins: A0JNH6, A0JNT9, A1A5D9, A5PJP1, A6NGB0, A7YWC8, B7ZNG0, O15049, O75154, O95996, P0C7N4, P58660, Q1LZF3, Q29RS0, Q2M1P5, Q2NL98, Q2TAC2, Q3LUD3, Q3TMW1, Q3UMT1, Q3V0F0, Q494R4, Q4QRL3, Q5ND29, Q5TZA2, Q6NSJ2, Q6NZW0, Q6PHN1, Q6QZQ4, Q6ZP65, Q7JVA5, Q8BP01, Q8C7U1, Q8CHW5, Q8CJ40, Q8N283, Q8N6Y0, Q8NFZ5, Q8TF21, Q91VJ2

Diamond homologs: A7YWC8, Q2NL98, Q6QZQ4, Q8BP01

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

362 predictions. Top by Δscore:

Variant	Effect	Δscore
19:5908818:T:A	acceptor_gain	1.0000
19:5908823:GTGA:G	acceptor_gain	1.0000
19:5909002:GC:G	donor_gain	1.0000
19:5905155:G:GT	donor_gain	0.9900
19:5908822:A:AG	acceptor_gain	0.9900
19:5908822:AGT:A	acceptor_gain	0.9900
19:5908823:G:GA	acceptor_gain	0.9900
19:5908823:GT:G	acceptor_gain	0.9900
19:5908823:GTG:G	acceptor_gain	0.9900
19:5905041:C:G	donor_gain	0.9800
19:5905067:T:TA	donor_gain	0.9800
19:5905077:GACCG:G	donor_gain	0.9800
19:5905082:G:GG	donor_gain	0.9800
19:5905117:GGCG:G	donor_gain	0.9800
19:5905118:GCGG:G	donor_gain	0.9800
19:5905147:A:T	donor_gain	0.9800
19:5909003:C:G	donor_gain	0.9800
19:5905077:G:GT	donor_gain	0.9700
19:5905078:ACCG:A	donor_loss	0.9700
19:5905081:GGTGA:G	donor_loss	0.9700
19:5905084:G:GG	donor_loss	0.9700
19:5908819:GCCA:G	acceptor_loss	0.9700
19:5908820:CCA:C	acceptor_loss	0.9700
19:5908821:CA:C	acceptor_loss	0.9700
19:5908821:CAGTG:C	acceptor_gain	0.9700
19:5908822:A:C	acceptor_loss	0.9700
19:5908822:AGTGA:A	acceptor_gain	0.9700
19:5908823:G:GG	acceptor_gain	0.9700
19:5908823:GTGAG:G	acceptor_gain	0.9700
19:5908824:T:TA	acceptor_gain	0.9700

AlphaMissense

1071 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:5904916:T:C	I9T	0.986
19:5904916:T:G	I9S	0.964
19:5904924:G:C	A12P	0.963
19:5904935:C:A	H15Q	0.938
19:5904935:C:G	H15Q	0.938
19:5904916:T:A	I9N	0.932
19:5905076:G:C	K62N	0.930
19:5905076:G:T	K62N	0.930
19:5908850:T:C	L73P	0.930
19:5904933:C:G	H15D	0.926
19:5909138:T:A	V169E	0.925
19:5904942:G:C	A18P	0.913
19:5904923:G:C	E11D	0.909
19:5904923:G:T	E11D	0.909
19:5904929:C:A	N13K	0.906
19:5904929:C:G	N13K	0.906
19:5904930:G:C	A14P	0.903
19:5904937:T:C	L16P	0.903
19:5904925:C:T	A12V	0.895
19:5904987:G:C	A33P	0.895
19:5904925:C:A	A12E	0.890
19:5908933:G:C	A101P	0.888
19:5904933:C:A	H15N	0.881
19:5908838:T:C	L69P	0.879
19:5904922:A:T	E11V	0.878
19:5904921:G:A	E11K	0.876
19:5904954:C:A	R22S	0.874
19:5904937:T:A	L16Q	0.873
19:5908922:T:C	L97S	0.868
19:5904928:A:T	N13I	0.867

dbSNP variants (sampled 300 via entrez): RS1000332987 (19:5908652 T>A), RS1000472025 (19:5903324 C>T), RS1000775171 (19:5903161 C>A,T), RS1001028204 (19:5908624 AT>A), RS1001074792 (19:5907431 G>A), RS1001242148 (19:5911218 T>C,G), RS1001400701 (19:5911097 A>G), RS1002455945 (19:5910074 C>T), RS1002609103 (19:5904644 C>A,T), RS1002983831 (19:5903057 T>C), RS1003413048 (19:5908740 G>A,T), RS1003981999 (19:5904149 C>T), RS1004192624 (19:5906570 T>C), RS1005088331 (19:5907677 T>C), RS1005423687 (19:5906222 A>G)

Disease associations

OMIM: gene MIM:617204 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003264_886	Post bronchodilator FEV1/FVC ratio	5.000000e-06
GCST003264_945	Post bronchodilator FEV1/FVC ratio	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004713	FEV/FVC ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Amiodarone	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Ozone	affects expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Okadaic Acid	decreases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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