YIPF7

protein-coding

Yip1 domain family member 7, the group of Yip1 domain containing

Gene summary

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and vesicle fusion with Golgi apparatus. Predicted to act upstream of or within Golgi organization. Predicted to be located in cis-Golgi network; endoplasmic reticulum membrane; and endoplasmic reticulum-Golgi intermediate compartment. Predicted to be active in trans-Golgi network. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_182592.3

Inheritance

—

ClinVar variants

U:46B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr4:44,622,088-44,678,556

External References & Databases

Ensembl (ENSG00000177752)

Transcript & Mutation Effects

hg38 • Region Span ~56.5 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 YIPF7 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 44

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182592.3. 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			2 clinvar			2
missense			43 clinvar	1 clinvar		44
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	1	0	47

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182592.3	RefSeq	NP_872398.3	5	MANE Select
ENST00000415895.9	Ensembl	ENSP00000412696.4	5	MANE Select
NM_001387382.1	RefSeq	NP_001374311.1	2	Standard
ENST00000332990.6	Ensembl	ENSP00000332772.6	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

endoplasmic reticulum membrane
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000332990
Coding exons: 6
Length: 56488
Individuals with no LoFs: 124390
Homozygous LoFs: 2
Heterozygous LoFs: 188
Defined: 124580
p: 0.000763

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.401	141	128	1.10	0.00000584	1793
Missense (PolyPhen)		55	49.321	1.1151		696
Synonymous	-1.44	60	47.4	1.27	0.00000250	522
Loss of Function	0.709	9	11.6	0.775	4.93e-7	161

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0089	0.0088	notable
Latino/Admixed American	0.00097	0.00096	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00056	0.00056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000046	0.000044	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.537
RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0326

Gene Damage Prediction

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