VNN1

vanin 1, the group of Vanin family

Basic information

Region (hg38): 6:132680848-132714055

Links

ENSG00000112299 ∙ NCBI:8876 ∙ OMIM:603570 ∙ HGNC:12705 ∙ Uniprot:O95497 ∙ 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 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	1	2
missense			25	7	5	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: gnomAD

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: 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

	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