YIF1B

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

Basic information

Region (hg38): 19:38303558-38317273

Links

ENSG00000167645 ∙ NCBI:90522 ∙ OMIM:619109 ∙ HGNC:30511 ∙ Uniprot:Q5BJH7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Kaya-Barakat-Masson syndrome (Moderate), mode of inheritance: AR
• Kaya-Barakat-Masson syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Kaya-Barakat-Masson syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	32006098; 33103737

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the YIF1B gene.

• Inborn_genetic_diseases (43 variants)
• not_provided (13 variants)
• Kaya-Barakat-Masson_syndrome (8 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• YIF1B-related_condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIF1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_001039672.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6		6
missense	1		46	1		48
nonsense	1					1
start loss						0
frameshift	3		1			4
splice donor/acceptor (+/-2bp)	2	1				3
Total	7	1	47	7	0

Highest pathogenic variant AF is 0.0000458543

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YIF1B	protein_coding	protein_coding	ENST00000339413	8	12161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000343	0.825	125719	0	27	125746	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	142	198	0.719	0.0000121	1994
Missense in Polyphen		42	49.854	0.84245		543
Synonymous	0.367	83	87.4	0.950	0.00000572	677
Loss of Function	1.29	9	14.3	0.631	7.05e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000276	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000127	0.000123
Middle Eastern	0.000276	0.000272
South Asian	0.0000654	0.0000653
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.438
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.245
• hipred: N
• hipred_score: 0.319
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yif1b

Gene ontology

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