VGLL1

vestigial like family member 1, the group of Vestigial like family|MicroRNA protein coding host genes

Basic information

Region (hg38): X:136532214-136556807

Links

ENSG00000102243 ∙ NCBI:51442 ∙ OMIM:300583 ∙ HGNC:20985 ∙ Uniprot:Q99990 ∙ 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 VGLL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VGLL1 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						0
missense			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in VGLL1

This is a list of pathogenic ClinVar variants found in the VGLL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-136536048-C-T		not specified	Uncertain significance (Jul 09, 2021)
X-136536196-C-A		not specified	Uncertain significance (Aug 01, 2022)
X-136548667-G-A		not specified	Uncertain significance (Dec 07, 2021)
X-136548669-G-A		not specified	Uncertain significance (Dec 20, 2023)
X-136548712-A-C		not specified	Uncertain significance (Jun 17, 2024)
X-136548751-G-A		not specified	Likely benign (Oct 26, 2021)
X-136548778-C-T		not specified	Uncertain significance (Oct 06, 2021)
X-136548828-G-A		not specified	Uncertain significance (Oct 06, 2023)
X-136548847-A-G		not specified	Uncertain significance (Dec 07, 2021)
X-136548943-G-A		not specified	Uncertain significance (Apr 24, 2023)
X-136548947-C-A		not specified	Uncertain significance (Mar 18, 2024)
X-136548996-G-A		not specified	Likely benign (May 27, 2022)
X-136550789-G-A		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VGLL1	protein_coding	protein_coding	ENST00000370634	4	24656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.814	0.182	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.494	95	110	0.867	0.00000919	1672
Missense in Polyphen		13	22.557	0.57632		405
Synonymous	-0.592	47	42.1	1.12	0.00000344	535
Loss of Function	2.18	0	5.55	0.00	3.51e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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:0000269|PubMed:10518497}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.522
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.673
• hipred: N
• hipred_score: 0.341
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vgll1

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus
• Molecular function: transcription coactivator activity