YIPF1

protein-coding

Yip1 domain family member 1, the group of Yip1 domain containing

Gene summary

Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Located in Golgi apparatus and transport vesicle. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018982.5

Inheritance

—

ClinVar variants

U:52B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr1:53,851,719-53,889,798

External References & Databases

Ensembl (ENSG00000058799)

Transcript & Mutation Effects

hg38 • Region Span ~38.1 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 YIPF1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 48

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018982.5. 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
missense			48 clinvar	1 clinvar		49
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	52	1	0	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018982.5	RefSeq	NP_061855.1	8	MANE Select
ENST00000072644.7	Ensembl	ENSP00000072644.1	8	MANE Select
ENST00000371399.5	Ensembl	ENSP00000360452.1	3	Standard
ENST00000371399.6	Ensembl	ENSP00000360452.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

vesicle-mediated transport

Molecular Function

protein binding
Rab GTPase binding

Cellular Component

Golgi trans cisterna
Golgi apparatus
Golgi medial cisterna
trans-Golgi network
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000072644
Coding exons: 8
Length: 39016
Individuals with no LoFs: 124927
Homozygous LoFs: 8
Heterozygous LoFs: 812
Defined: 125747
p: 0.00327

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.144	173	168	1.03	0.00000856	1988
Missense (PolyPhen)		56	68.997	0.81163		807
Synonymous	1.45	46	60.4	0.762	0.00000317	602
Loss of Function	2.26	7	17.1	0.410	8.93e-7	196

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.00070	0.00069	rare
Ashkenazi Jewish	0.015	0.015	notable
East Asian	0.00016	0.00016	rare
Finnish	0.0068	0.0067	notable
European (Non-Finnish)	0.0031	0.0031	notable
South Asian	0.0039	0.0038	notable
Other	0.0033	0.0033	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.462
RVIS EVS: -0.23
RVIS percentile EVS: 37.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.189

Gene Damage Prediction

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