OIP5

Chr 15

Opa interacting protein 5

Also known as: 5730547N13Rik, CT86, LINT-25, MIS18B, MIS18beta, hMIS18beta

NCBI Gene: 11339 ENSG00000104147 UniProt: O43482 OMIM: 606020

The protein encoded by this gene localizes to centromeres, where it is essential for recruitment of CENP-A through the mediator Holliday junction recognition protein. Expression of this gene is upregulated in several cancers, making it a putative therapeutic target. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.76

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.76LOEUF

pLI 0.000

Z-score -0.26

OE 1.09 (0.67–1.76)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-1.31Z-score

OE missense 1.32 (1.17–1.50)

171 obs / 129.2 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.09 (0.67–1.76)

0≤0.351.4

Missense OE?1.32 (1.17–1.50)

0≤0.61.4

Synonymous OE?1.12

0≤1.21.6

LoF obs/exp: 10 / 9.2Missense obs/exp: 171 / 129.2Syn Z: -0.71

Background carrier burden — how many people carry a rare variant somewhere in OIP5?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

359 rare PASS variants

Rare truncating (LoF)

1 in 580

83 rare PASS variants

Rare synonymous (reference)

1 in 380

155 rare PASS variants

Rare missense and truncating variants are carried at similar rates in OIP5; this gene does not show strong loss-of-function constraint by this measure. 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 210	1 in 670
South Asian	~43k	1 in 130	1 in 810
Remaining (unassigned)	~30k	1 in 130	1 in 450
European (Finnish)	~27k	1 in 370	≈ 1 in 6,400
Admixed American	~22k	1 in 140	1 in 800
African / African American	~21k	1 in 110	1 in 1,500
East Asian	~20k	1 in 210	1 in 2,800
Ashkenazi Jewish	~13k	1 in 1,100	none seen
Middle Eastern	~2,884	1 in 120	1 in 480

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 4 of 5 coding exons well covered in gnomAD exomes; exon 4 marginal. Genomes: all 5.? see exons ↓