YIF1B

Chr 19

Yip1 interacting factor homolog B, membrane trafficking protein

Also known as: FinGER8, KABAMAS

NCBI Gene: 90522 ENSG00000167645 UniProt: Q5BJH7

The protein functions in endoplasmic reticulum to Golgi vesicle transport and plays a key role in targeting receptors to neuronal dendrites and in primary cilium assembly. Biallelic mutations cause Kaya-Barakat-Masson syndrome, an autosomal recessive disorder. This gene is not highly constrained against loss-of-function variants.

GeneReviews ResearchSummary from RefSeq, OMIM, UniProt

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]

GeneReviews ResearchGenerating clinical summary…

DNmechanismLOEUF 1.10

Clinical Summary— YIF1B

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Gene-Disease Validity (ClinGen)

Kaya-Barakat-Masson syndrome · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

9 unique Pathogenic / Likely Pathogenic· 78 VUS of 123 total submissions

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GeneReview available — YIF1B

Authoritative clinical overview · Recommended first read

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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.10LOEUF

pLI 0.000

Z-score 1.29

OE 0.63 (0.38–1.10)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.40Z-score

OE missense 0.72 (0.63–0.83)

142 obs / 197.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.63 (0.38–1.10)

0≤0.351.4

Missense OE?0.72 (0.63–0.83)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 9 / 14.3Missense obs/exp: 142 / 197.5Syn Z: 0.37

This gene — mechanism propensity

0.7132th %ile

GOF

0.5562th %ile

LOF

0.3746th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

123 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic8

Likely Pathogenic1

VUS78

Likely Benign9

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Synonymous	Total
Pathogenic	7	1	0	8
Likely Pathogenic	1	0	0	1
VUS	1	76	1	78
Likely Benign	0	1	8	9
Benign	0	0	0	0
Total	9	78	9	96

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

9 pathogenic / likely-pathogenic (of 12) ClinVar copy-number / structural variants overlap YIF1B — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →