YIF1A

protein-coding

Yip1 interacting factor homolog A, membrane trafficking protein, the group of YIP family

Gene summary

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Located in Golgi apparatus and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

YIF1

MANE transcript

NM_020470.3

Inheritance

—

ClinVar variants

U:65B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr11:66,284,572-66,289,184

External References & Databases

Ensembl (ENSG00000174851)

Transcript & Mutation Effects

hg38 • Region Span ~4.6 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 YIF1A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 62

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020470.3. 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	2 clinvar		3
missense			59 clinvar	1 clinvar		60
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	65	3	0	68

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020470.3	RefSeq	NP_065203.2	8	MANE Select
ENST00000376901.9	Ensembl	ENSP00000366098.4	8	MANE Select
NM_001300861.2	RefSeq	NP_001287790.1	7	Standard
ENST00000359461.10	Ensembl	ENSP00000352437.6	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

XBP1(S) activates chaperone genes

Biological Process

protein transport
IRE1-mediated unfolded protein response

Molecular Function

protein binding

Cellular Component

endoplasmic reticulum membrane
endoplasmic reticulum-Golgi intermediate compartment
COPII-coated ER to Golgi transport vesicle
integral component of Golgi membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376901
Coding exons: 8
Length: 4591
Individuals with no LoFs: 125632
Homozygous LoFs: 0
Heterozygous LoFs: 105
Defined: 125737
p: 0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.392	201	186	1.08	0.0000116	1871
Missense (PolyPhen)		68	60.672	1.1208		632
Synonymous	-0.120	82	80.6	1.02	0.00000538	630
Loss of Function	-0.0719	14	13.7	1.02	5.87e-7	161

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00075	0.00075	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00034	0.00033	rare
South Asian	0.00078	0.00078	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possible role in transport between endoplasmic reticulum and Golgi. {ECO:0000269|PubMed:15990086}.;

Recessive Scores

pRec: 0.121

Intolerance Scores

LoFtool: 0.837
RVIS EVS: -0.6
RVIS percentile EVS: 17.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.819

Gene Damage Prediction

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