VIT

protein-coding

vitrin

Gene summary

This gene encodes an extracellular matrix (ECM) protein. The protein may be associated with cell adhesion and migration. High levels of expression of the protein in specific parts of the brain suggest its likely role in neural development. [provided by RefSeq, Jun 2016]

MANE transcript

NM_053276.4

Inheritance

—

ClinVar variants

U:145B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.23

Max pathogenic AF

—

Genomic locus

chr2:36,696,690-36,814,794

External References & Databases

Ensembl (ENSG00000205221)

Transcript & Mutation Effects

hg38 • Region Span ~118.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VIT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_053276.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			141 clinvar	5 clinvar		146
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	145	6	1	152

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_053276.4	RefSeq	NP_444506.2	15	MANE Select
ENST00000379242.8	Ensembl	ENSP00000368544.3	15	MANE Select
NM_001177969.2	RefSeq	NP_001171440.1	14	Standard
NM_001177970.2	RefSeq	NP_001171441.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

growth plate cartilage chondrocyte morphogenesis
positive regulation of cell-substrate adhesion
spinal cord development
extracellular matrix organization

Molecular Function

glycosaminoglycan binding

Cellular Component

interstitial matrix
extracellular space
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379242
Coding exons: 15
Length: 118103
Individuals with no LoFs: 125627
Homozygous LoFs: 1
Heterozygous LoFs: 120
Defined: 125748
p: 0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.77	511	410	1.25	0.0000236	4499
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00092	0.00092	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00038	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00060	0.00059	rare
South Asian	0.00069	0.00065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.182

Gene Damage Prediction

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