SIGLECL1
protein-codingSIGLEC family like 1, the group of Ig-like cell adhesion molecule family
Gene summary
Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]
- C19orf75
- SIGLEC23P
- SIGLECP7
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~23.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SIGLECL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001385465.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 21 | 3 | 24 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 4 | 0 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001372394.1 | 5 | MANE Select | |
| Ensembl | ENSP00000469601.2 | 5 | MANE Select | |
| RefSeq | NP_001295366.1 | 4 | Standard | |
| RefSeq | NP_001372395.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000316401
- Coding exons
- 5
- Length
- 22982
- Individuals with no LoFs
- 125497
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 248
- Defined
- 125746
- p
- 0.000991
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.718 | 88 | 109 | 0.807 | 0.00000572 | 1274 |
| Missense (PolyPhen) | 14 | 25.758 | 0.54352 | 331 | ||
| Synonymous | 0.103 | 43 | 43.9 | 0.980 | 0.00000261 | 394 |
| Loss of Function | -0.510 | 10 | 8.41 | 1.19 | 3.55e-7 | 102 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00043 | 0.00043 | rare |
| Ashkenazi Jewish | 0.0073 | 0.0074 | notable |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00099 | 0.00097 | rare |
| South Asian | 0.0013 | 0.0012 | notable |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 56.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |