SERINC1
protein-codingserine incorporator 1
Gene summary
Predicted to enable acetyltransferase activator activity; enzyme binding activity; and protein-macromolecule adaptor activity. Predicted to be involved in membrane biogenesis; phosphatidylserine metabolic process; and sphingolipid metabolic process. Predicted to be located in endoplasmic reticulum membrane and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]
- TDE2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.5 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 SERINC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020755.4. 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 | 2 | 3 | |||
| missense | 50 | 50 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 56 | 2 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065806.1 | 10 | MANE Select | |
| Ensembl | ENSP00000342962.3 | 10 | MANE Select | |
| Ensembl | ENSP00000580784.1 | 8 | Standard | |
| Ensembl | ENSP00000580785.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Sphingolipid Metabolism
- Metabolism of amino acids and derivatives
- Metabolism
- Amino acid synthesis and interconversion (transamination)
- Serine biosynthesis
Biological Process
- phosphatidylserine metabolic process
- sphingolipid metabolic process
- phospholipid biosynthetic process
- membrane biogenesis
- positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity
Molecular Function
- protein binding
- enzyme binding
- protein binding, bridging
Cellular Component
- endoplasmic reticulum membrane
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339697
- Coding exons
- 10
- Length
- 28469
- Individuals with no LoFs
- 125718
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125736
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.36 | 176 | 234 | 0.751 | 0.0000115 | 2942 |
| Missense (PolyPhen) | 50 | 85.253 | 0.58649 | 1154 | ||
| Synonymous | -0.180 | 85 | 82.9 | 1.03 | 0.00000430 | 863 |
| Loss of Function | 3.00 | 8 | 23.8 | 0.337 | 0.00000117 | 297 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000067 | 0.000062 | rare |
| Latino/Admixed American | 0.000063 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Enhances the incorporation of serine into phosphatidylserine and sphingolipids. {ECO:0000250|UniProtKB:Q7TNK0}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- RVIS EVS
- 0.28
- RVIS percentile EVS
- 71.41
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.415
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |