SIGLEC15

Chr 18

sialic acid binding Ig like lectin 15

Also known as: CD33L3, HsT1361, SIGLEC-15

NCBI Gene: 284266ENSG00000197046UniProt: Q6ZMC9

Predicted to be involved in regulation of actin cytoskeleton organization; regulation of bone resorption; and regulation of osteoclast development. Predicted to be located in membrane. Predicted to be part of protein-containing complex. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Research Assistant →
0
Active trials
12
Pubs (1 yr)
49
P/LP submissions
0%
P/LP missense
1.87
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— SIGLEC15
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
47 unique Pathogenic / Likely Pathogenic· 65 VUS of 126 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.87LOEUF
pLI 0.000
Z-score -0.77
OE 1.29 (0.80–1.87)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.98Z-score
OE missense 0.79 (0.69–0.91)
139 obs / 175.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE1.29 (0.80–1.87)
0≤0.351.4
Missense OE0.79 (0.69–0.91)
0≤0.61.4
Synonymous OE0.83
0≤1.21.6
LoF obs/exp: 11 / 8.6Missense obs/exp: 139 / 175.5Syn Z: 1.20
DN
0.6939th %ile
GOF
0.6442th %ile
LOF
0.3844th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

126 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic45
Likely Pathogenic2
VUS65
Likely Benign9
Benign2
45
Pathogenic
2
Likely Pathogenic
65
VUS
9
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
45
0
45
Likely Pathogenic
0
0
2
0
2
VUS
0
60
5
0
65
Likely Benign
0
4
1
4
9
Benign
0
1
0
1
2
Total065535123

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SIGLEC15 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients