YIF1A

Chr 11

Yip1 interacting factor homolog A, membrane trafficking protein

Also known as: 54TM, FinGER7, YIF1, YIF1P

NCBI Gene: 10897 ENSG00000174851 UniProt: O95070 OMIM: 611484

The protein is involved in vesicle-mediated transport between the endoplasmic reticulum and Golgi apparatus. Mutations cause autosomal recessive intellectual disability with microcephaly and variable congenital anomalies. This gene is not highly constrained against loss-of-function variants.

OMIM ResearchSummary from RefSeq, UniProt

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

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.58

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.58LOEUF

pLI 0.000

Z-score -0.07

OE 1.02 (0.67–1.58)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.39Z-score

OE missense 1.08 (0.96–1.22)

201 obs / 186.0 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.02 (0.67–1.58)

0≤0.351.4

Missense OE?1.08 (0.96–1.22)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 14 / 13.7Missense obs/exp: 201 / 186.0Syn Z: -0.12

Background carrier burden — how many people carry a rare variant somewhere in YIF1A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 91

490 rare PASS variants

Rare truncating (LoF)

1 in 1,100

102 rare PASS variants

Rare synonymous (reference)

1 in 300

166 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for YIF1A. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 120	1 in 1,600
South Asian	~43k	1 in 76	1 in 680
Remaining (unassigned)	~30k	1 in 95	1 in 770
European (Finnish)	~27k	1 in 700	1 in 820
Admixed American	~22k	1 in 85	1 in 590
African / African American	~21k	1 in 81	1 in 420
East Asian	~20k	1 in 82	1 in 1,000
Ashkenazi Jewish	~13k	1 in 790	1 in 330
Middle Eastern	~2,884	1 in 130	1 in 280

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 8 coding exons well covered in gnomAD exomes and genomes.? see exons ↓