VIT

vitrin

Basic information

Region (hg38): 2:36696690-36814794

Links

ENSG00000205221 ∙ NCBI:5212 ∙ OMIM:617693 ∙ HGNC:12697 ∙ Uniprot:Q6UXI7 ∙ 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 VIT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VIT 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
missense			44	3		47
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6			6
Total	0	0	50	4	1

Variants in VIT

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

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

Position	Type	Phenotype	Significance	ClinVar
2-36716386-C-T		not specified	Uncertain significance (Jan 03, 2022)
2-36729432-T-C		not specified	Uncertain significance (May 31, 2023)
2-36743100-C-A		not specified	Uncertain significance (Jun 28, 2023)
2-36743122-T-A		not specified	Uncertain significance (Sep 27, 2021)
2-36743132-G-A		not specified	Uncertain significance (Oct 12, 2021)
2-36743238-G-C		not specified	Uncertain significance (Jan 31, 2024)
2-36743243-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-36754976-T-G		not specified	Uncertain significance (Jan 17, 2024)
2-36755001-A-G		not specified	Uncertain significance (Feb 28, 2023)
2-36755024-C-A		not specified	Uncertain significance (Oct 04, 2022)
2-36755028-G-T		not specified	Uncertain significance (Jun 26, 2023)
2-36767112-A-G		not specified	Uncertain significance (Mar 01, 2023)
2-36767189-G-A		not specified	Uncertain significance (Dec 03, 2021)
2-36767193-C-G		not specified	Uncertain significance (Mar 17, 2023)
2-36767236-C-T			Likely benign (Mar 01, 2022)
2-36767244-T-C		not specified	Uncertain significance (Dec 20, 2021)
2-36773813-C-G			Benign (Aug 01, 2018)
2-36775023-C-T		not specified	Uncertain significance (Apr 27, 2023)
2-36775062-G-A		not specified	Uncertain significance (Apr 23, 2024)
2-36775067-G-C			Likely benign (Jul 15, 2018)
2-36781754-C-T		not specified	Uncertain significance (Jun 06, 2023)
2-36783370-A-G		not specified	Uncertain significance (Jul 14, 2021)
2-36787137-A-G		not specified	Likely benign (Jan 17, 2023)
2-36787147-C-T		not specified	Uncertain significance (Jun 02, 2023)
2-36787154-A-C		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VIT	protein_coding	protein_coding	ENST00000379242	15	118103

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.44e-32	0.00000130	125627	1	120	125748	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.77	511	410	1.25	0.0000236	4499
Missense in Polyphen		172	142.36	1.2082		1516
Synonymous	-1.16	185	166	1.11	0.0000111	1388
Loss of Function	-1.27	43	34.9	1.23	0.00000182	400

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00118
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000599	0.000589
Middle Eastern	0.000381	0.000381
South Asian	0.000693	0.000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes matrix assembly and cell adhesiveness. Plays a role in spinal cord formation by regulating the proliferation and differentiation of neural stem cells. {ECO:0000250|UniProtKB:Q8VHI5}.

Recessive Scores

• pRec: 0.190

Intolerance Scores

• loftool: 0.0965
• rvis_EVS: -0.68
• rvis_percentile_EVS: 15.39

Haploinsufficiency Scores

• pHI: 0.610
• hipred: N
• hipred_score: 0.251
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.182

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vit
• Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Biological process: growth plate cartilage chondrocyte morphogenesis;positive regulation of cell-substrate adhesion;spinal cord development;extracellular matrix organization
• Cellular component: interstitial matrix;extracellular space;extracellular matrix
• Molecular function: glycosaminoglycan binding