YIPF3

protein-coding

Yip1 domain family member 3, the group of Yip1 domain containing

Gene summary

Predicted to be involved in cell differentiation. Located in Golgi apparatus and transport vesicle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf109

MANE transcript

NM_015388.4

Inheritance

—

ClinVar variants

U:66B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr6:43,511,832-43,516,985

External References & Databases

Ensembl (ENSG00000137207)

Transcript & Mutation Effects

hg38 • Region Span ~5.2 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 YIPF3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015388.4. 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	6 clinvar		8
missense			57 clinvar	2 clinvar		59
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	66	8	0	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015388.4	RefSeq	NP_056203.2	9	MANE Select
ENST00000372422.7	Ensembl	ENSP00000361499.2	9	MANE Select
ENST00000416380.6	Ensembl	ENSP00000390056.2	2	Standard
ENST00000455768.6	Ensembl	ENSP00000392699.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell differentiation

Molecular Function

protein binding

Cellular Component

Golgi apparatus
plasma membrane
integral component of membrane
transport vesicle
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372422
Coding exons: 9
Length: 5164
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125748
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.625	186	212	0.879	0.0000117	2248
Missense (PolyPhen)		47	66.67	0.70497		710
Synonymous	-0.763	94	85.0	1.11	0.00000495	730
Loss of Function	2.95	5	18.8	0.266	9.87e-7	192

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the maintenance of the Golgi structure. May play a role in hematopoiesis. {ECO:0000269|PubMed:12490290, ECO:0000269|PubMed:21757827}.;

Recessive Scores

pRec: 0.143

Intolerance Scores

LoFtool: 0.450
RVIS EVS: -0.54
RVIS percentile EVS: 20.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.933

Gene Damage Prediction

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