YIPF2

protein-coding

Yip1 domain family member 2, 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_001321439.2

Inheritance

—

ClinVar variants

U:71B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr19:10,922,185-10,928,681

External References & Databases

Ensembl (ENSG00000130733)

Transcript & Mutation Effects

hg38 • Region Span ~6.5 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 YIPF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001321439.2. 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			2 clinvar	1 clinvar		3
missense			68 clinvar	5 clinvar		73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	71	6	0	77

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 84 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001321439.2	RefSeq	NP_001308368.1	8	MANE Select
ENST00000586748.6	Ensembl	ENSP00000466055.1	8	MANE Select
NM_001321440.2	RefSeq	NP_001308369.1	7	Standard
NM_024029.5	RefSeq	NP_076934.1	8	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: ENST00000586748
Coding exons: 8
Length: 5914
Individuals with no LoFs: 125623
Homozygous LoFs: 0
Heterozygous LoFs: 107
Defined: 125730
p: 0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.142	197	191	1.03	0.0000121	1996
Missense (PolyPhen)		70	69.239	1.011		802
Synonymous	0.418	85	90.0	0.944	0.00000601	679
Loss of Function	0.727	13	16.2	0.805	6.91e-7	179

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00081	0.00081	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00049	0.00047	rare
South Asian	0.00043	0.00042	rare
Other	0.00082	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.383
RVIS EVS: -0.2
RVIS percentile EVS: 38.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.908

Gene Damage Prediction

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