YIF1B

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

Basic information

Region (hg38): 19:38303557-38317273

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.

• Kaya-Barakat-Masson syndrome (3 variants)
• not provided (2 variants)
• Inborn genetic diseases (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.

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				5		5
missense			22			22
nonsense	1					1
start loss						0
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region				1		1
non coding			1			1
Total	3	0	24	5	0

Highest pathogenic variant AF is 0.0000526

Variants in YIF1B

This is a list of pathogenic ClinVar variants found in the YIF1B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38304861-C-A		not specified	Uncertain significance (Sep 27, 2021)
19-38305412-C-T		Inborn genetic diseases	Uncertain significance (Jan 06, 2021)
19-38305414-T-C		Inborn genetic diseases	Uncertain significance (Sep 28, 2022)
19-38305436-GTTCCGGGCCCCACGCACCGG-CTGCGTCT			Uncertain significance (Mar 19, 2022)
19-38305447-C-T		Inborn genetic diseases	Uncertain significance (Jun 05, 2023)
19-38305469-T-C			Likely benign (Apr 01, 2023)
19-38305479-G-C		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
19-38306958-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
19-38307501-A-T		Inborn genetic diseases	Uncertain significance (Jul 24, 2020)
19-38307523-T-G		Kaya-Barakat-Masson syndrome	Pathogenic (Jul 20, 2022)
19-38307599-G-A			Likely benign (Jul 01, 2022)
19-38307632-G-A			Likely benign (Jan 01, 2024)
19-38307650-G-T		Inborn genetic diseases	Uncertain significance (Jun 13, 2024)
19-38307661-C-A		Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
19-38307671-G-T			Uncertain significance (Jan 21, 2020)
19-38307682-T-C		Inborn genetic diseases	Uncertain significance (Feb 09, 2022)
19-38307694-C-A		Kaya-Barakat-Masson syndrome	Pathogenic (Dec 02, 2022)
19-38307723-G-T			Uncertain significance (Jan 21, 2020)
19-38307749-G-A			Likely benign (May 01, 2023)
19-38308791-C-T		Kaya-Barakat-Masson syndrome	Pathogenic (Jan 14, 2022)
19-38308997-G-A		Kaya-Barakat-Masson syndrome	Uncertain significance (Mar 29, 2024)
19-38309013-G-C			Likely benign (Nov 01, 2023)
19-38309021-C-A		Inborn genetic diseases	Uncertain significance (Dec 16, 2023)
19-38309229-G-A		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
19-38309259-T-G		Kaya-Barakat-Masson syndrome	Pathogenic (Dec 17, 2020)

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