VNN3P

vanin 3, pseudogene, the group of Vanin family

Basic information

Region (hg38): 6:132722926-132734692

Previous symbols: [ "VNN3" ]

Links

ENSG00000093134

∙ NCBI:55350 ∙ OMIM:606592 ∙ HGNC:16431 ∙ ∙ ∙ 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 VNN3P gene.

not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VNN3P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1 clinvar	1
Total	0	0	0	0	1

Variants in VNN3P

This is a list of pathogenic ClinVar variants found in the VNN3P region.

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

Position	Type	Phenotype	Significance	ClinVar
6-132724775-T-G			Benign (Apr 18, 2018)	776162

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VNN3P	protein_coding	protein_coding	ENST00000427187	4	11979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00433	0.879	125719	0	24	125743	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.481	126	112	1.13	0.00000535	1351
Missense in Polyphen		28	25.786	1.0859		323
Synonymous	0.224	40	41.8	0.956	0.00000215	395
Loss of Function	1.33	5	9.39	0.533	3.96e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000119	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000368	0.000326

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:11491533}.;
Pathway: Pantothenate and CoA biosynthesis - Homo sapiens (human);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Haploinsufficiency Scores

pHI: 0.0597
hipred: N
hipred_score: 0.112
ghis: 0.485

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.429

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Vnn3
Phenotype

Gene ontology

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