VPS9D1

protein-coding

VPS9 domain containing 1, the group of VPS9 domain containing

Gene summary

Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in proton motive force-driven ATP synthesis. Predicted to be active in cytosol and endocytic vesicle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C16orf7

MANE transcript

NM_004913.3

Inheritance

—

ClinVar variants

U:149B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr16:89,707,134-89,720,898

External References & Databases

Ensembl (ENSG00000075399)

Transcript & Mutation Effects

hg38 • Region Span ~13.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VPS9D1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004913.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	2 clinvar	4
missense			139 clinvar	3 clinvar		142
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	149	4	2	155

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004913.3	RefSeq	NP_004904.2	15	MANE Select
ENST00000389386.8	Ensembl	ENSP00000374037.3	15	MANE Select
ENST00000561976.5	Ensembl	ENSP00000454244.1	13	Standard
ENST00000561976.6	Ensembl	ENSP00000454244.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ATP synthesis coupled proton transport
positive regulation of GTPase activity

Molecular Function

GTPase activator activity
transporter activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389386
Coding exons: 15
Length: 13853
Individuals with no LoFs: 124772
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 124806
p: 0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.151	364	356	1.02	0.0000223	3926
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00021	0.00019	rare
Latino/Admixed American	0.00030	0.00026	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.18
RVIS percentile EVS: 40.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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