YIF1B

protein-coding

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

Gene summary

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

MANE transcript

NM_001039672.3

Inheritance

ClinVar variants

P:9U:64B:8

Top phenotype

Kaya-Barakat-Masson syndrome

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr19:38,303,558-38,317,273

External References & Databases

Ensembl (ENSG00000167645)

Transcript & Mutation Effects

hg38 • Region Span ~13.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Kaya-Barakat-Masson syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0030878

Submitter: ClinGen

The *YIF1B* gene, located on chromosome 19 at 19q13.2, encodes a trafficking protein that belongs to the FinGER protein family and is involved in endoplasmic reticulum-to-Golgi trafficking. *YIF1B* was first reported in relation to autosomal recessive Kaya-Barakat-Masson syndrome (KABAMAS) in 2020 (Diaz et al. 2020, PMID: 33103737; AlMuhaizea et al. 2020, PMID: 32006098). KABAMAS is a severe neurodevelopmental disorder characterized by profoundly impaired global development with variable motor abnormalities, poor coordination resulting in the inability to sit or walk, impaired intellectual development with absent speech, poor eye contact, and feeding difficulties resulting in poor overall growth. More variable features include early-onset seizures, ocular anomalies, foot deformities, and nonspecific brain imaging findings. Dysmorphic features are generally not present. The disease generally presents at birth and may be lethal in infancy or childhood. The mechanism of disease is reported to be loss of function. At least ten unique variants (2 missense, 2 nonsense, 3 frameshift, 3 splice-site) that have been reported in 13 probands from four publications (PMIDs: 32006098, 33103737, 36435927, 36948290) are included in this curation. Most of the variants identified were homozygous occurrences in consanguineous families. More evidence is available in the literature (PMID: 34373908), but the maximum score allowed for genetic evidence has been reached (12 pts). This gene-disease relationship is also supported by expression data, functional alteration studies, and a *Yif1b* knockout mouse model (PMIDs: 18685031, 26077767, 32006098, 33103737). In summary, there is definitive evidence to support the relationship between *YIF1B* and autosomal recessive Kaya-Barakat-Masson syndrome. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Syndromic GCEP on the meeting date August 16th, 2024 (SOP Version 10).

Kaya-Barakat-Masson syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0030878

Submitter: Ambry Genetics

Kaya-Barakat-Masson syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030878

Submitter: PanelApp Australia

Kaya-Barakat-Masson syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030878

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Kaya-Barakat-Masson syndromeAR

Manifestation: Neurologic; Ophthalmologic

Intervention: General

Rationale: 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

Refs: 32006098; 33103737

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to YIF1B variants in ClinVar

5 Conditions Cataloged

Inborn genetic diseasesTotal: 49

not providedTotal: 16

Kaya-Barakat-Masson syndromeTotal: 12

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

YIF1B-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039672.3. 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	7 clinvar		9
missense	1 clinvar		54 clinvar	1 clinvar		56
nonsense	1 clinvar		1 clinvar			2
start loss						0
frameshift	3 clinvar		1 clinvar			4
splice donor/acceptor (+/-2bp)	3 clinvar	1 clinvar	6 clinvar			10
Total	8	1	64	8	0	81

Highest pathogenic variant AF is 0.000045854333

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039672.3	RefSeq	NP_001034761.1	8	MANE Select
ENST00000339413.11	Ensembl	ENSP00000343435.5	8	MANE Select
NM_001039671.3	RefSeq	NP_001034760.1	8	Standard
NM_001039673.3	RefSeq	NP_001034762.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase

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: ENST00000339413
Coding exons: 8
Length: 12161
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125746
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.40	142	198	0.719	0.0000121	1994
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000090	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.000065	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.438
RVIS EVS: -0.36
RVIS percentile EVS: 28.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.367

Gene Damage Prediction

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