SERINC3
protein-codingserine incorporator 3
Gene summary
Enables phospholipid scramblase activity. Involved in antiviral innate immune response and plasma membrane phospholipid scrambling. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
- TDE1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.9 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 SERINC3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006811.4. 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 | 1 | 2 | |||
| missense | 66 | 8 | 74 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 72 | 9 | 0 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006802.1 | 10 | MANE Select | |
| Ensembl | ENSP00000340243.4 | 10 | MANE Select | |
| RefSeq | NP_945179.1 | 10 | Standard | |
| Ensembl | ENSP00000255175.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of amino acids and derivatives
- Metabolism
- Amino acid synthesis and interconversion (transamination)
- Serine biosynthesis
Biological Process
- L-serine biosynthetic process
- phosphatidylserine metabolic process
- sphingolipid metabolic process
- detection of virus
- L-serine transport
Molecular Function
- L-serine transmembrane transporter activity
Cellular Component
- Golgi membrane
- plasma membrane
- integral component of membrane
- perinuclear region of cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000342374
- Coding exons
- 10
- Length
- 25889
- Individuals with no LoFs
- 125706
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 42
- Defined
- 125748
- p
- 0.000167
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.162 | 258 | 265 | 0.972 | 0.0000139 | 3096 |
| Missense (PolyPhen) | 84 | 102.35 | 0.82075 | 1280 | ||
| Synonymous | 0.741 | 89 | 98.3 | 0.905 | 0.00000533 | 925 |
| Loss of Function | 3.62 | 4 | 22.6 | 0.177 | 0.00000111 | 267 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00014 | 0.00012 | rare |
| Latino/Admixed American | 0.00020 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.00027 | 0.00026 | rare |
| South Asian | 0.000073 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Restriction factor required to restrict infectivity of lentiviruses, such as HIV-1: acts by inhibiting an early step of viral infection. Impairs the penetration of the viral particle into the cytoplasm (PubMed:26416733, PubMed:26416734). {ECO:0000269|PubMed:26416733, ECO:0000269|PubMed:26416734}.;
Recessive Scores
- pRec
- 0.169
Intolerance Scores
- LoFtool
- 0.747
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 42.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.774
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |