GOLIM4

Chr 3

golgi integral membrane protein 4

Also known as: GIMPC, GOLPH4, GPP130, P138

NCBI Gene: 27333 ENSG00000173905 UniProt: O00461 OMIM: 606805

The Golgi complex plays a key role in the sorting and modification of proteins exported from the endoplasmic reticulum. The protein encoded by this gene is a type II Golgi-resident protein. It may process proteins synthesized in the rough endoplasmic reticulum and assist in the transport of protein cargo through the Golgi apparatus. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.73

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.73LOEUF

pLI 0.000

Z-score 3.05

OE 0.52 (0.38–0.73)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.10Z-score

OE missense 0.98 (0.90–1.07)

360 obs / 365.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.52 (0.38–0.73)

0≤0.351.4

Missense OE?0.98 (0.90–1.07)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 25 / 47.7Missense obs/exp: 360 / 365.6Syn Z: -0.29

Background carrier burden — how many people carry a rare variant somewhere in GOLIM4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 68

894 rare PASS variants

Rare truncating (LoF)

1 in 1,300

156 rare PASS variants

Rare synonymous (reference)

1 in 220

349 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GOLIM4. 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 69	1 in 1,500
South Asian	~43k	1 in 67	1 in 820
Remaining (unassigned)	~30k	1 in 60	1 in 1,300
European (Finnish)	~27k	1 in 130	1 in 950
Admixed American	~22k	1 in 76	1 in 790
African / African American	~21k	1 in 51	1 in 1,300
East Asian	~20k	1 in 63	1 in 1,100
Ashkenazi Jewish	~13k	1 in 340	1 in 810
Middle Eastern	~2,884	1 in 84	≈ 1 in 940

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): 10 of 16 coding exons well covered in gnomAD exomes; exon 3 poorly covered; exons 2, 4, 6, 11, 12 marginal. Genomes: all 16.? see exons ↓