YIF1A

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

Basic information

Region (hg38): 11:66284572-66289184

Previous symbols: [ "YIF1" ]

Links

ENSG00000174851 ∙ NCBI:10897 ∙ OMIM:611484 ∙ HGNC:16688 ∙ Uniprot:O95070 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the YIF1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIF1A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	0

Variants in YIF1A

This is a list of pathogenic ClinVar variants found in the YIF1A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-66284641-C-T		not specified	Uncertain significance (Sep 23, 2023)
11-66284720-G-A		not specified	Uncertain significance (Jul 14, 2024)
11-66284726-G-A		not specified	Uncertain significance (Jan 07, 2025)
11-66284728-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-66284732-C-T		not specified	Uncertain significance (Sep 27, 2021)
11-66284750-C-T		not specified	Uncertain significance (Oct 24, 2023)
11-66284773-A-C		not specified	Uncertain significance (Sep 15, 2021)
11-66284779-C-T		not specified	Uncertain significance (Jan 25, 2023)
11-66284910-G-A		not specified	Uncertain significance (Dec 21, 2024)
11-66284916-T-C		not specified	Uncertain significance (May 28, 2024)
11-66284926-C-T		not specified	Uncertain significance (Mar 31, 2024)
11-66284953-C-T		not specified	Uncertain significance (Mar 20, 2024)
11-66285385-C-T		not specified	Uncertain significance (Feb 22, 2023)
11-66285390-T-A		not specified	Uncertain significance (Mar 15, 2024)
11-66285390-T-C		not specified	Uncertain significance (Jul 20, 2021)
11-66285436-G-A		not specified	Uncertain significance (Mar 20, 2024)
11-66285440-G-A		not specified	Likely benign (Feb 01, 2025)
11-66285528-G-A		not specified	Uncertain significance (Aug 30, 2021)
11-66285739-G-A		not specified	Likely benign (May 20, 2024)
11-66285758-G-A		not specified	Uncertain significance (Jan 30, 2024)
11-66287606-T-C		not specified	Uncertain significance (May 08, 2024)
11-66287624-A-G		not specified	Uncertain significance (Jan 31, 2024)
11-66287633-C-G		not specified	Uncertain significance (Dec 12, 2023)
11-66287633-C-T		not specified	Uncertain significance (Jul 29, 2023)
11-66287654-C-A		not specified	Uncertain significance (Sep 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YIF1A	protein_coding	protein_coding	ENST00000376901	8	4591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.18e-10	0.0696	125632	0	105	125737	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.392	201	186	1.08	0.0000116	1871
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00125
Ashkenazi Jewish	0.000399	0.000397
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000337	0.000334
Middle Eastern	0.000163	0.000163
South Asian	0.000785	0.000784
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible role in transport between endoplasmic reticulum and Golgi. {ECO:0000269|PubMed:15990086}.
• Pathway: XBP1(S) activates chaperone genes (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.837
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.339
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.819

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yif1a

Gene ontology

• Biological process: protein transport;IRE1-mediated unfolded protein response
• Cellular component: endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;COPII-coated ER to Golgi transport vesicle;integral component of Golgi membrane
• Molecular function: protein binding