VNN1

vanin 1, the group of Vanin family

Basic information

Region (hg38): 6:132680849-132714055

Links

ENSG00000112299NCBI:8876OMIM:603570HGNC:12705Uniprot:O95497AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VNN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VNN1 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
clinvar
1
clinvar
2
missense
25
clinvar
7
clinvar
5
clinvar
37
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 25 8 6

Variants in VNN1

This is a list of pathogenic ClinVar variants found in the VNN1 region.

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

Position Type Phenotype Significance ClinVar
6-132683142-A-G Benign (Aug 16, 2018)776156
6-132683157-A-G not specified Uncertain significance (Mar 28, 2022)2231269
6-132683169-C-T not specified Likely benign (Mar 31, 2022)2281173
6-132683289-G-T not specified Uncertain significance (Dec 17, 2023)3188716
6-132683307-G-A not specified Uncertain significance (Apr 24, 2024)3332126
6-132683316-T-C not specified Uncertain significance (Apr 06, 2024)3332129
6-132683322-C-T not specified Uncertain significance (Dec 28, 2023)3188715
6-132684349-G-A not specified Uncertain significance (Jul 12, 2022)2300723
6-132684359-A-G Likely benign (Jul 10, 2018)749805
6-132684361-T-G not specified Uncertain significance (Feb 05, 2024)3188714
6-132684400-C-T not specified Likely benign (Sep 27, 2022)2308778
6-132684475-T-C not specified Likely benign (Nov 08, 2022)2351329
6-132692293-A-G Benign (Jul 31, 2018)776157
6-132692437-G-T Benign (Aug 16, 2018)776158
6-132692444-T-C not specified Uncertain significance (Mar 29, 2023)2531430
6-132692506-G-A not specified Uncertain significance (Jan 10, 2022)2271491
6-132692510-G-A not specified Uncertain significance (Jun 07, 2023)2558410
6-132692523-C-G Benign (Aug 16, 2018)776159
6-132692560-G-A not specified Uncertain significance (Apr 07, 2023)2534817
6-132692563-T-A not specified Uncertain significance (Dec 06, 2021)2265324
6-132692587-G-A Benign (Aug 16, 2018)776160
6-132693116-A-G not specified Uncertain significance (Mar 16, 2022)2373078
6-132693153-C-G not specified Likely benign (Sep 15, 2021)2360178
6-132693158-G-A not specified Uncertain significance (Jun 12, 2023)2559416
6-132693167-T-C not specified Uncertain significance (Nov 18, 2022)2327401

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
VNN1protein_codingprotein_codingENST00000367928 732460
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000004390.8521256640821257460.000326
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.06772832801.010.00001423355
Missense in Polyphen107103.561.03321286
Synonymous0.1411031050.9820.00000566998
Loss of Function1.441117.50.6297.36e-7235

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001100.00110
Ashkenazi Jewish0.00009930.0000992
East Asian0.0001660.000163
Finnish0.00009240.0000924
European (Non-Finnish)0.0002050.000202
Middle Eastern0.0001660.000163
South Asian0.0006210.000621
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Amidohydrolase that hydrolyzes specifically one of the carboamide linkages in D-pantetheine thus recycling pantothenic acid (vitamin B5) and releasing cysteamine. {ECO:0000269|PubMed:10567687, ECO:0000269|PubMed:11491533, ECO:0000269|PubMed:25478849}.;
Pathway
Pantothenate and CoA biosynthesis - Homo sapiens (human);Pantothenate and CoA Biosynthesis;Neutrophil degranulation;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Vitamin B5 - CoA biosynthesis from pantothenate;Innate Immune System;Immune System;Metabolism;Vitamin B5 (pantothenate) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

pRec
0.180

Intolerance Scores

loftool
0.194
rvis_EVS
1.47
rvis_percentile_EVS
95.26

Haploinsufficiency Scores

pHI
0.287
hipred
N
hipred_score
0.112
ghis
0.417

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.780

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Vnn1
Phenotype
homeostasis/metabolism phenotype;

Gene ontology

Biological process
acute inflammatory response;chronic inflammatory response;inflammatory response;response to oxidative stress;pantothenate metabolic process;positive regulation of T cell differentiation in thymus;neutrophil degranulation;innate immune response;cell-cell adhesion;negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
Cellular component
extracellular region;plasma membrane;integral component of membrane;anchored component of membrane;azurophil granule membrane
Molecular function
pantetheine hydrolase activity