SCAMP2

Chr 15

secretory carrier membrane protein 2

NCBI Gene: 10066 ENSG00000140497 UniProt: O15127 OMIM: 606912

This gene product belongs to the SCAMP family of proteins which are secretory carrier membrane proteins. They function as carriers to the cell surface in post-golgi recycling pathways. Different family members are highly related products of distinct genes, and are usually expressed together. These findings suggest that the SCAMPs may function at the same site during vesicular transport rather than in separate pathways. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.55

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.55LOEUF

pLI 0.160

Z-score 3.00

OE 0.26 (0.14–0.55)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.30Z-score

OE missense 0.73 (0.63–0.84)

130 obs / 178.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.26 (0.14–0.55)

0≤0.351.4

Missense OE?0.73 (0.63–0.84)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 5 / 19.2Missense obs/exp: 130 / 178.8Syn Z: 0.19

Background carrier burden — how many people carry a rare variant somewhere in SCAMP2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

455 rare PASS variants

Rare truncating (LoF)

1 in 1,500

83 rare PASS variants

Rare synonymous (reference)

1 in 210

190 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SCAMP2. 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 160	1 in 1,900
South Asian	~43k	1 in 140	1 in 2,200
Remaining (unassigned)	~30k	1 in 120	1 in 1,300
European (Finnish)	~27k	1 in 700	≈ 1 in 6,400
Admixed American	~22k	1 in 92	1 in 500
African / African American	~21k	1 in 70	1 in 2,200
East Asian	~20k	1 in 160	1 in 1,200
Ashkenazi Jewish	~13k	1 in 220	none seen
Middle Eastern	~2,884	1 in 92	none seen

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): 8 of 9 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 9.? see exons ↓