GOLM2

Chr 15

golgi membrane protein 2

Also known as: CASC4, H63

NCBI Gene: 113201 ENSG00000166734 UniProt: Q6P4E1

The increased expression level of this gene is associated with HER-2/neu proto-oncogene overexpression. Amplification and resulting overexpression of this proto-oncogene are found in approximately 30% of human breast and 20% of human ovarian cancers. Alternatively spliced variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Dec 2010]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.74

LOEUF

Mechanism· predicted

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?

0.74LOEUF

pLI 0.000

Z-score 2.53

OE 0.45 (0.28–0.74)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.13Z-score

OE missense 0.79 (0.70–0.90)

186 obs / 234.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.45 (0.28–0.74)

0≤0.351.4

Missense OE?0.79 (0.70–0.90)

0≤0.61.4

Synonymous OE?0.76

0≤1.21.6

LoF obs/exp: 11 / 24.5Missense obs/exp: 186 / 234.8Syn Z: 1.76

Background carrier burden — how many people carry a rare variant somewhere in GOLM2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 150

517 rare PASS variants

Rare truncating (LoF)

1 in 3,800

59 rare PASS variants

Rare synonymous (reference)

1 in 220

182 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GOLM2. 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 240	1 in 3,100
South Asian	~43k	1 in 120	1 in 4,200
Remaining (unassigned)	~30k	1 in 120	≈ 1 in 10,000
European (Finnish)	~27k	1 in 440	≈ 1 in 13,000
Admixed American	~22k	1 in 120	1 in 3,700
African / African American	~21k	1 in 75	1 in 3,400
East Asian	~20k	1 in 140	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 620	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 92	≈ 1 in 1,400

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): 5 of 10 coding exons well covered in gnomAD exomes; exons 2, 3, 4, 7, 8 marginal. Genomes: all 10.? see exons ↓