VNN2

vanin 2, the group of Vanin family

Basic information

Region (hg38): 6:132743869-132763459

Links

ENSG00000112303 ∙ NCBI:8875 ∙ OMIM:603571 ∙ HGNC:12706 ∙ Uniprot:O95498 ∙ 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 VNN2 gene.

• Inborn genetic diseases (23 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VNN2 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						0
missense			22	3	3	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	3

Variants in VNN2

This is a list of pathogenic ClinVar variants found in the VNN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-132744311-C-T		not specified	Uncertain significance (Nov 15, 2021)
6-132744319-T-G		not specified	Uncertain significance (Jul 26, 2022)
6-132744320-G-T		not specified	Uncertain significance (May 09, 2023)
6-132744383-C-T		not specified	Uncertain significance (Jun 11, 2021)
6-132744386-A-G		not specified	Uncertain significance (May 31, 2023)
6-132744398-G-C		not specified	Uncertain significance (Mar 29, 2023)
6-132744475-C-T		not specified	Uncertain significance (Aug 26, 2022)
6-132749813-G-T		not specified	Uncertain significance (Apr 22, 2022)
6-132749816-C-T		not specified	Likely benign (Nov 09, 2023)
6-132749832-A-C		not specified	Uncertain significance (Dec 20, 2022)
6-132751156-C-T		not specified	Uncertain significance (Mar 01, 2024)
6-132751167-C-T			Benign (Jan 25, 2018)
6-132751180-C-T		not specified	Uncertain significance (Sep 26, 2023)
6-132751198-C-T		not specified	Uncertain significance (Apr 04, 2023)
6-132751227-A-T		not specified	Uncertain significance (Dec 20, 2023)
6-132751228-T-C		not specified	Uncertain significance (Aug 08, 2022)
6-132751329-C-A		not specified	Uncertain significance (Feb 16, 2023)
6-132751489-T-G		not specified	Uncertain significance (Apr 26, 2023)
6-132752566-C-A		not specified	Uncertain significance (Jun 24, 2022)
6-132752658-G-A		not specified	Uncertain significance (Aug 02, 2023)
6-132752672-C-A			Likely benign (Jan 01, 2023)
6-132755923-A-G		not specified	Uncertain significance (Aug 10, 2021)
6-132755930-G-T		Malignant tumor of prostate	Uncertain significance (-)
6-132755934-C-T		not specified	Uncertain significance (Dec 20, 2023)
6-132755941-T-C		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VNN2	protein_coding	protein_coding	ENST00000326499	7	19590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.45e-15	0.00656	125583	0	162	125745	0.000644

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.467	299	277	1.08	0.0000134	3391
Missense in Polyphen		86	85.633	1.0043		1106
Synonymous	-0.469	111	105	1.06	0.00000549	1031
Loss of Function	-0.374	21	19.2	1.09	9.64e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00114	0.00112
Ashkenazi Jewish	0.00	0.00
East Asian	0.00148	0.00147
Finnish	0.00	0.00
European (Non-Finnish)	0.000725	0.000721
Middle Eastern	0.00148	0.00147
South Asian	0.000812	0.000719
Other	0.000822	0.000815

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. Involved in the thymus homing of bone marrow cells. May regulate beta-2 integrin-mediated cell adhesion, migration and motility of neutrophil. {ECO:0000269|PubMed:11491533}.
• Pathway: Pantothenate and CoA biosynthesis - Homo sapiens (human);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Metabolism;Vitamin B5 (pantothenate) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.21

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.112
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.900

Gene Damage Prediction

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

Gene ontology

• Biological process: pantothenate metabolic process
• Cellular component: extracellular region;plasma membrane;anchored component of membrane
• Molecular function: pantetheine hydrolase activity