VGLL4

vestigial like family member 4, the group of Vestigial like family

Basic information

Region (hg38): 3:11556069-11771350

Links

ENSG00000144560 ∙ NCBI:9686 ∙ OMIM:618692 ∙ HGNC:28966 ∙ Uniprot:Q14135 ∙ 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 VGLL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VGLL4 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	23	1	0

Variants in VGLL4

This is a list of pathogenic ClinVar variants found in the VGLL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-11558592-C-G		not specified	Uncertain significance (Dec 18, 2023)
3-11558627-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-11558756-C-T		not specified	Uncertain significance (Nov 18, 2023)
3-11558818-G-T		not specified	Uncertain significance (Jun 10, 2024)
3-11559346-C-T		not specified	Uncertain significance (Aug 28, 2023)
3-11559362-C-T		not specified	Uncertain significance (Jan 02, 2024)
3-11559427-G-A		not specified	Uncertain significance (Dec 06, 2021)
3-11564828-G-A		not specified	Uncertain significance (Jan 02, 2024)
3-11564835-C-G		not specified	Uncertain significance (Jan 03, 2024)
3-11564840-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-11564850-C-T		not specified	Uncertain significance (May 27, 2022)
3-11564851-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
3-11564868-T-C		not specified	Uncertain significance (Jan 17, 2024)
3-11564909-G-A		not specified	Uncertain significance (Mar 23, 2022)
3-11564910-T-C		not specified	Likely benign (Nov 03, 2023)
3-11564925-C-T		not specified	Uncertain significance (Feb 06, 2024)
3-11564935-C-T		not specified	Uncertain significance (Apr 04, 2023)
3-11564955-G-A		not specified	Uncertain significance (Jan 31, 2023)
3-11564970-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-11564982-G-A		not specified	Uncertain significance (Feb 10, 2023)
3-11564994-G-A		not specified	Uncertain significance (Apr 25, 2022)
3-11601879-C-T		not specified	Uncertain significance (Mar 23, 2022)
3-11601942-G-A		not specified	Uncertain significance (Apr 13, 2022)
3-11601948-C-T		not specified	Uncertain significance (Aug 05, 2023)
3-11601980-G-T		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VGLL4	protein_coding	protein_coding	ENST00000430365	5	164677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0728	0.878	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	176	186	0.945	0.0000124	1930
Missense in Polyphen		69	77.481	0.89055		765
Synonymous	-1.60	98	79.8	1.23	0.00000621	592
Loss of Function	1.67	3	8.12	0.369	3.44e-7	112

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)	0.0000365	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a specific coactivator for the mammalian TEFs. {ECO:0000250}.

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.244
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.361
• hipred: N
• hipred_score: 0.332
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.721

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vgll4

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: protein binding