VGLL3

protein-coding

vestigial like family member 3, the group of Vestigial like family

Gene summary

Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016206.4

Inheritance

—

ClinVar variants

U:46B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr3:86,876,388-86,991,149

External References & Databases

Ensembl (ENSG00000206538)

Transcript & Mutation Effects

hg38 • Region Span ~114.8 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 VGLL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016206.4. 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				2 clinvar		2
missense			45 clinvar	2 clinvar		47
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	4	0	50

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016206.4	RefSeq	NP_057290.2	4	MANE Select
ENST00000398399.7	Ensembl	ENSP00000381436.2	4	MANE Select
NM_001320493.2	RefSeq	NP_001307422.1	4	Standard
NM_001320494.2	RefSeq	NP_001307423.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398399
Coding exons: 4
Length: 53151
Individuals with no LoFs: 124797
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 124807
p: 0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.217	175	183	0.955	0.00000938	2113
Missense (PolyPhen)		28	47.594	0.58831		589
Synonymous	-0.869	79	69.8	1.13	0.00000371	649
Loss of Function	2.19	4	12.3	0.325	6.06e-7	147

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a specific coactivator for the mammalian TEFs. {ECO:0000250|UniProtKB:Q8N8G2}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.340
RVIS EVS: 0.13
RVIS percentile EVS: 63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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