VMAC

vimentin type intermediate filament associated coiled-coil protein

Basic information

Region (hg38): 19:5904872-5910853

Links

ENSG00000187650 ∙ NCBI:400673 ∙ OMIM:617204 ∙ HGNC:33803 ∙ Uniprot:Q2NL98 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VMAC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VMAC gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	1

Variants in VMAC

This is a list of pathogenic ClinVar variants found in the VMAC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-5904919-G-A		not specified	Uncertain significance (Jun 30, 2022)
19-5904929-C-A		not specified	Uncertain significance (Nov 01, 2021)
19-5904931-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-5904952-G-C		not specified	Uncertain significance (Jan 10, 2023)
19-5904964-A-C		not specified	Uncertain significance (Apr 19, 2023)
19-5905000-T-C		not specified	Uncertain significance (Apr 07, 2022)
19-5905003-A-G		not specified	Likely benign (Mar 03, 2022)
19-5905018-G-T		not specified	Uncertain significance (Oct 27, 2023)
19-5905024-C-A		not specified	Uncertain significance (May 31, 2023)
19-5905080-C-T		not specified	Uncertain significance (Mar 12, 2024)
19-5908837-C-T		not specified	Uncertain significance (Nov 08, 2021)
19-5908839-C-T			Benign (Dec 31, 2019)
19-5908906-G-A		not specified	Likely benign (May 23, 2023)
19-5908961-G-A		not specified	Uncertain significance (Dec 13, 2022)
19-5908964-G-A		not specified	Uncertain significance (Oct 29, 2021)
19-5908987-G-T		not specified	Uncertain significance (Apr 07, 2022)
19-5908996-G-A		not specified	Uncertain significance (Jun 23, 2023)
19-5909009-G-A		not specified	Uncertain significance (Mar 07, 2024)
19-5909014-G-A		not specified	Uncertain significance (Apr 05, 2023)
19-5909024-C-T		not specified	Uncertain significance (Oct 05, 2021)
19-5909032-G-A		not specified	Uncertain significance (Dec 28, 2023)
19-5909035-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-5909038-G-A		not specified	Likely benign (Apr 04, 2024)
19-5909053-G-A		not specified	Uncertain significance (May 30, 2024)
19-5909095-G-T		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VMAC	protein_coding	protein_coding	ENST00000339485	2	5996

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0414	0.672	125436	0	10	125446	0.0000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.263	75	81.7	0.918	0.00000472	1038
Missense in Polyphen		20	22.543	0.88719		368
Synonymous	0.0409	37	37.3	0.991	0.00000210	390
Loss of Function	0.497	2	2.92	0.686	1.25e-7	39

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000585	0.0000585
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000618
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.336

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vmac

Gene ontology

• Cellular component: cytoplasm;type III intermediate filament