VGLL2

vestigial like family member 2, the group of Vestigial like family

Basic information

Region (hg38): 6:117265558-117273565

Links

ENSG00000170162 ∙ NCBI:245806 ∙ OMIM:609979 ∙ HGNC:20232 ∙ Uniprot:Q8N8G2 ∙ 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 VGLL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VGLL2 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			18		2	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	3

Variants in VGLL2

This is a list of pathogenic ClinVar variants found in the VGLL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-117268185-C-G		not specified	Uncertain significance (Jun 03, 2022)
6-117268199-C-A			Benign (Dec 31, 2019)
6-117268251-G-A		not specified	Uncertain significance (Apr 10, 2023)
6-117268350-C-T		not specified	Uncertain significance (Oct 31, 2023)
6-117268392-G-C		not specified	Uncertain significance (Feb 28, 2024)
6-117268401-G-A		not specified	Uncertain significance (Jan 03, 2024)
6-117268457-C-A		not specified	Uncertain significance (Jun 22, 2024)
6-117268482-C-G			Benign (Dec 13, 2018)
6-117270572-T-G		not specified	Uncertain significance (Dec 08, 2023)
6-117270618-C-A			Benign (Dec 13, 2018)
6-117270660-C-T		not specified	Uncertain significance (Nov 14, 2023)
6-117270702-G-A		not specified	Uncertain significance (Jul 20, 2021)
6-117270745-C-G		not specified	Uncertain significance (Jan 11, 2023)
6-117270759-A-G		not specified	Uncertain significance (May 21, 2024)
6-117270760-C-G		not specified	Uncertain significance (May 14, 2024)
6-117270798-C-G		not specified	Uncertain significance (May 11, 2022)
6-117270845-G-C		not specified	Uncertain significance (Dec 16, 2023)
6-117270849-C-G		not specified	Uncertain significance (Apr 16, 2024)
6-117270890-G-A		not specified	Uncertain significance (Dec 18, 2023)
6-117270908-C-G		not specified	Uncertain significance (Nov 08, 2022)
6-117270920-G-T		not specified	Uncertain significance (Feb 28, 2024)
6-117270968-G-A		not specified	Uncertain significance (Nov 19, 2022)
6-117271017-G-T		not specified	Uncertain significance (Oct 12, 2021)
6-117271023-C-T		not specified	Uncertain significance (Jul 20, 2021)
6-117271038-A-G		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VGLL2	protein_coding	protein_coding	ENST00000326274	4	8008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.705	0.291	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.117	121	125	0.970	0.00000565	2010
Missense in Polyphen		49	44.442	1.1026		712
Synonymous	0.440	49	53.1	0.923	0.00000249	644
Loss of Function	2.35	1	8.32	0.120	3.57e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a specific coactivator for the mammalian TEFs. May play a role in the development of skeletal muscles.

Recessive Scores

• pRec: 0.118

Haploinsufficiency Scores

• pHI: 0.273
• hipred: Y
• hipred_score: 0.807
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.561

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vgll2

Zebrafish Information Network

• Gene name: vgll2a
• Affected structure: cranial neural crest cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: skeletal muscle tissue development;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm
• Molecular function: transcription coactivator activity;protein binding;protein C-terminus binding