VRTN

vertebrae development associated

Basic information

Region (hg38): 14:74303069-74360008

Previous symbols: [ "C14orf115" ]

Links

ENSG00000133980 ∙ NCBI:55237 ∙ ∙ HGNC:20223 ∙ Uniprot:Q9H8Y1 ∙ 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 VRTN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VRTN 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			32	2	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	2

Variants in VRTN

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

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

Position	Type	Phenotype	Significance	ClinVar
14-74303138-C-T			Benign (Jun 29, 2018)
14-74303196-T-A			Likely benign (Mar 17, 2021)
14-74303274-G-A			Benign (Jul 07, 2018)
14-74356826-C-A		not specified	Uncertain significance (Feb 12, 2024)
14-74357336-C-T		not specified	Uncertain significance (Nov 06, 2023)
14-74357337-G-A		not specified	Uncertain significance (Mar 22, 2023)
14-74357363-C-T		not specified	Uncertain significance (Dec 01, 2022)
14-74357423-G-A		not specified	Likely benign (Feb 03, 2023)
14-74357496-C-T		not specified	Uncertain significance (May 20, 2024)
14-74357601-T-C		not specified	Uncertain significance (May 11, 2022)
14-74357610-G-A		not specified	Uncertain significance (Jun 17, 2024)
14-74357639-T-G		not specified	Uncertain significance (Aug 22, 2023)
14-74357675-C-T		not specified	Uncertain significance (Jun 02, 2023)
14-74357708-A-G		not specified	Uncertain significance (Jul 06, 2021)
14-74357714-G-A		not specified	Uncertain significance (Aug 02, 2021)
14-74357724-T-C		not specified	Uncertain significance (Apr 17, 2023)
14-74357760-G-A		not specified	Uncertain significance (Mar 07, 2023)
14-74357767-C-T			Benign (Nov 15, 2017)
14-74357768-G-A		not specified	Uncertain significance (Jan 17, 2024)
14-74357794-G-C		not specified	Uncertain significance (Feb 02, 2022)
14-74357795-C-T		not specified	Uncertain significance (Aug 22, 2023)
14-74357814-G-A		not specified	Uncertain significance (Sep 17, 2021)
14-74357856-G-A		not specified	Uncertain significance (Aug 16, 2022)
14-74357961-C-T		not specified	Uncertain significance (Nov 23, 2021)
14-74357994-G-A		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VRTN	protein_coding	protein_coding	ENST00000256362	1	56940

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0110	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	348	448	0.778	0.0000300	4478
Missense in Polyphen		103	186.89	0.55112		1839
Synonymous	0.813	174	188	0.925	0.0000114	1547
Loss of Function	3.71	1	18.0	0.0556	7.71e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.54

Haploinsufficiency Scores

• pHI: 0.654
• hipred: Y
• hipred_score: 0.626
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vrtn
• Phenotype: growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); skeleton phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: vrtn
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: transposition, DNA-mediated
• Molecular function: transposase activity;sequence-specific DNA binding