VRTN

protein-coding

vertebrae development associated

Gene summary

Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be active in chromatin. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf115

MANE transcript

NM_018228.3

Inheritance

—

ClinVar variants

U:106B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr14:74,303,069-74,360,008

External References & Databases

Ensembl (ENSG00000133980)

Transcript & Mutation Effects

hg38 • Region Span ~56.9 kb

Loading mutation effect viewer...

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 VRTN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 110

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018228.3. 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
missense			106 clinvar	5 clinvar	1 clinvar	112
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	106	5	2	113

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018228.3	RefSeq	NP_060698.2	1	MANE Select
ENST00000256362.5	Ensembl	ENSP00000256362.4	1	MANE Select
ENST00000557177.1	Ensembl	ENSP00000452158.1	1	Standard
ENST00000925859.1	Ensembl	ENSP00000595918.1	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
vrtn	Danio rerio	Structure: head Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

vrtn

Danio rerio

Structure: head

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transposition, DNA-mediated

Molecular Function

transposase activity
sequence-specific DNA binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000256362
Coding exons: 1
Length: 56940
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125747
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	348	448	0.778	0.0000300	4478
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.35
RVIS percentile EVS: 29.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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