VNN1
Basic information
Region (hg38): 6:132680849-132714055
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 2 | |||||
missense | 25 | 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) | |||
6-132683157-A-G | not specified | Uncertain significance (Mar 28, 2022) | ||
6-132683169-C-T | not specified | Likely benign (Mar 31, 2022) | ||
6-132683289-G-T | not specified | Uncertain significance (Dec 17, 2023) | ||
6-132683307-G-A | not specified | Uncertain significance (Apr 24, 2024) | ||
6-132683316-T-C | not specified | Uncertain significance (Apr 06, 2024) | ||
6-132683322-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
6-132684349-G-A | not specified | Uncertain significance (Jul 12, 2022) | ||
6-132684359-A-G | Likely benign (Jul 10, 2018) | |||
6-132684361-T-G | not specified | Uncertain significance (Feb 05, 2024) | ||
6-132684400-C-T | not specified | Likely benign (Sep 27, 2022) | ||
6-132684475-T-C | not specified | Likely benign (Nov 08, 2022) | ||
6-132692293-A-G | Benign (Jul 31, 2018) | |||
6-132692437-G-T | Benign (Aug 16, 2018) | |||
6-132692444-T-C | not specified | Uncertain significance (Mar 29, 2023) | ||
6-132692506-G-A | not specified | Uncertain significance (Jan 10, 2022) | ||
6-132692510-G-A | not specified | Uncertain significance (Jun 07, 2023) | ||
6-132692523-C-G | Benign (Aug 16, 2018) | |||
6-132692560-G-A | not specified | Uncertain significance (Apr 07, 2023) | ||
6-132692563-T-A | not specified | Uncertain significance (Dec 06, 2021) | ||
6-132692587-G-A | Benign (Aug 16, 2018) | |||
6-132693116-A-G | not specified | Uncertain significance (Mar 16, 2022) | ||
6-132693153-C-G | not specified | Likely benign (Sep 15, 2021) | ||
6-132693158-G-A | not specified | Uncertain significance (Jun 12, 2023) | ||
6-132693167-T-C | not specified | Uncertain significance (Nov 18, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
VNN1 | protein_coding | protein_coding | ENST00000367928 | 7 | 32460 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000439 | 0.852 | 125664 | 0 | 82 | 125746 | 0.000326 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0677 | 283 | 280 | 1.01 | 0.0000142 | 3355 |
Missense in Polyphen | 107 | 103.56 | 1.0332 | 1286 | ||
Synonymous | 0.141 | 103 | 105 | 0.982 | 0.00000566 | 998 |
Loss of Function | 1.44 | 11 | 17.5 | 0.629 | 7.36e-7 | 235 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00110 | 0.00110 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000166 | 0.000163 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.000205 | 0.000202 |
Middle Eastern | 0.000166 | 0.000163 |
South Asian | 0.000621 | 0.000621 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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