VPS9D1

VPS9 domain containing 1, the group of VPS9 domain containing

Basic information

Region (hg38): 16:89707133-89720898

Previous symbols: [ "C16orf7" ]

Links

ENSG00000075399 ∙ NCBI:9605 ∙ OMIM:619292 ∙ HGNC:13526 ∙ Uniprot:Q9Y2B5 ∙ 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 VPS9D1 gene.

• Inborn genetic diseases (33 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS9D1 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			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	2	1

Variants in VPS9D1

This is a list of pathogenic ClinVar variants found in the VPS9D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-89707880-C-T		not specified	Likely benign (May 18, 2022)
16-89708452-C-A		not specified	Uncertain significance (Dec 06, 2022)
16-89708455-C-T		not specified	Uncertain significance (Apr 05, 2023)
16-89708467-C-T		not specified	Uncertain significance (Jul 14, 2021)
16-89708482-C-T		not specified	Uncertain significance (Aug 30, 2022)
16-89708878-G-A		not specified	Uncertain significance (Dec 12, 2023)
16-89708885-C-T		not specified	Uncertain significance (Oct 30, 2023)
16-89708911-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-89709254-A-G		not specified	Uncertain significance (Oct 13, 2021)
16-89709292-G-T		not specified	Uncertain significance (Mar 20, 2023)
16-89709293-C-T		not specified	Uncertain significance (Dec 01, 2022)
16-89709314-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-89709365-C-T		not specified	Uncertain significance (Aug 26, 2022)
16-89709418-C-T		not specified	Uncertain significance (Mar 24, 2023)
16-89709819-G-A		not specified	Uncertain significance (Nov 22, 2021)
16-89709849-T-C		not specified	Uncertain significance (Aug 11, 2022)
16-89709864-T-G		not specified	Uncertain significance (Jan 10, 2023)
16-89710631-G-C		not specified	Uncertain significance (Oct 29, 2021)
16-89710700-C-A		not specified	Uncertain significance (Sep 01, 2021)
16-89710808-G-A		not specified	Uncertain significance (Jan 02, 2024)
16-89710861-G-A		not specified	Uncertain significance (Dec 14, 2023)
16-89710906-C-T		not specified	Uncertain significance (Aug 16, 2021)
16-89710937-C-A		not specified	Uncertain significance (Aug 22, 2023)
16-89710958-A-G		not specified	Uncertain significance (Apr 25, 2023)
16-89710978-C-T		not specified	Likely benign (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS9D1	protein_coding	protein_coding	ENST00000389386	15	13853

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.21e-20	0.00361	124772	0	34	124806	0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.151	364	356	1.02	0.0000223	3926
Missense in Polyphen		91	108.67	0.83736		1233
Synonymous	-1.78	202	172	1.17	0.0000121	1347
Loss of Function	0.169	30	31.0	0.967	0.00000159	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000507	0.000490
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000113	0.000111
Finnish	0.0000477	0.0000464
European (Non-Finnish)	0.000155	0.000150
Middle Eastern	0.000113	0.000111
South Asian	0.00	0.00
Other	0.000172	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.45

Haploinsufficiency Scores

• pHI: 0.0503
• hipred: N
• hipred_score: 0.414
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vps9d1

Gene ontology

• Biological process: ATP synthesis coupled proton transport;positive regulation of GTPase activity
• Molecular function: GTPase activator activity;transporter activity