VPS72

vacuolar protein sorting 72 homolog, the group of SRCAP complex|Tip60/Nua4 histone acetyltransferase complex subunits

Basic information

Region (hg38): 1:151176304-151195321

Previous symbols: [ "TCFL1" ]

Links

ENSG00000163159

∙ NCBI:6944 ∙ OMIM:600607 ∙ HGNC:11644 ∙ Uniprot:Q15906 ∙ 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 VPS72 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS72 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in VPS72

This is a list of pathogenic ClinVar variants found in the VPS72 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151176802-C-T		not specified	Uncertain significance (Oct 27, 2021)	2355627
1-151178016-T-G		not specified	Uncertain significance (Jun 18, 2021)	3189038

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS72	protein_coding	protein_coding	ENST00000354473	6	25335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000202	0.979	125713	0	34	125747	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	169	237	0.712	0.0000150	2384
Missense in Polyphen		37	71.849	0.51497		740
Synonymous	0.820	81	90.9	0.891	0.00000516	811
Loss of Function	2.05	9	18.5	0.485	0.00000128	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Deposition-and-exchange histone chaperone specific for H2AFZ, specifically chaperones H2AFZ and deposits it into nucleosomes. As component of the SRCAP complex, mediates the ATP- dependent exchange of histone H2AFZ/H2B dimers for nucleosomal H2A/H2B, leading to transcriptional regulation of selected genes by chromatin remodeling. {ECO:0000269|PubMed:26974126}.;
Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.145

Intolerance Scores

loftool: 0.242
rvis_EVS: 0.22
rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

pHI: 0.277
hipred: Y
hipred_score: 0.696
ghis: 0.501

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.834

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Vps72
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;somatic stem cell population maintenance;histone exchange
Cellular component: nucleus;nucleoplasm;nuclear speck;protein-containing complex
Molecular function: DNA binding;protein binding;histone binding