VGLL3

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

Basic information

Region (hg38): 3:86876388-86991149

Links

ENSG00000206538 ∙ NCBI:389136 ∙ OMIM:609980 ∙ HGNC:24327 ∙ Uniprot:A8MV65 ∙ 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 VGLL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VGLL3 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				2		2
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	0

Variants in VGLL3

This is a list of pathogenic ClinVar variants found in the VGLL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-86968637-G-C		not specified	Uncertain significance (Mar 04, 2024)
3-86968640-C-A		not specified	Uncertain significance (Dec 18, 2023)
3-86968650-C-T		not specified	Uncertain significance (May 03, 2023)
3-86968710-G-A		not specified	Uncertain significance (Aug 08, 2022)
3-86968746-G-A		not specified	Uncertain significance (Jan 04, 2022)
3-86968770-A-T		not specified	Uncertain significance (Jan 22, 2024)
3-86968776-C-A		not specified	Uncertain significance (Feb 09, 2023)
3-86968812-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-86968857-C-T		not specified	Uncertain significance (Aug 04, 2023)
3-86968884-C-T		not specified	Uncertain significance (Dec 09, 2023)
3-86968905-G-T		not specified	Uncertain significance (Jun 18, 2021)
3-86968934-G-A		not specified	Uncertain significance (Dec 14, 2021)
3-86969057-G-A		not specified	Uncertain significance (Mar 18, 2024)
3-86969057-G-T		not specified	Uncertain significance (Aug 02, 2021)
3-86969099-C-T		not specified	Uncertain significance (Mar 25, 2024)
3-86969100-G-A		not specified	Uncertain significance (Feb 05, 2024)
3-86969120-C-T		not specified	Uncertain significance (Feb 27, 2023)
3-86978548-C-A		not specified	Uncertain significance (Aug 02, 2022)
3-86978565-T-A		not specified	Uncertain significance (Apr 20, 2024)
3-86978691-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-86978700-G-T		not specified	Uncertain significance (Oct 24, 2023)
3-86978702-T-G		not specified	Uncertain significance (Oct 24, 2023)
3-86978704-T-C			Likely benign (May 01, 2023)
3-86990639-C-T			Likely benign (Jul 01, 2022)
3-86990641-G-T		not specified	Uncertain significance (Nov 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VGLL3	protein_coding	protein_coding	ENST00000398399	4	53151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0697	0.918	124797	0	10	124807	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.217	175	183	0.955	0.00000938	2113
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000180	0.000180
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0694
• hipred: N
• hipred_score: 0.214
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vgll3

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus