SERINC2

protein-coding

serine incorporator 2

Gene summary

Enables phospholipid scramblase activity. Involved in plasma membrane phospholipid scrambling. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TDE2L

MANE transcript

NM_178865.5

Inheritance

—

ClinVar variants

U:106B:10

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr1:31,409,565-31,434,680

External References & Databases

Ensembl (ENSG00000168528)

Transcript & Mutation Effects

hg38 • Region Span ~25.1 kb

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GenCC 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 SERINC2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 95

not providedTotal: 6

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178865.5. 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 clinvar	1 clinvar	2
missense			100 clinvar	6 clinvar	1 clinvar	107
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar		1 clinvar	3
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	106	7	3	116

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178865.5	RefSeq	NP_849196.2	10	MANE Select
ENST00000373709.8	Ensembl	ENSP00000362813.3	10	MANE Select
NM_001199037.2	RefSeq	NP_001185966.1	10	Standard
NM_001199038.2	RefSeq	NP_001185967.1	11	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

phosphatidylserine metabolic process
sphingolipid metabolic process
positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity
positive regulation of serine C-palmitoyltransferase activity

Cellular Component

integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373710
Coding exons: 11
Length: 25114
Individuals with no LoFs: 125511
Homozygous LoFs: 0
Heterozygous LoFs: 237
Defined: 125748
p: 0.000943

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.262	315	302	1.04	0.0000196	3024
Missense (PolyPhen)		156	139.74	1.1164		1435
Synonymous	-0.688	142	132	1.08	0.00000951	918
Loss of Function	0.610	21	24.2	0.866	0.00000104	256

Population LoF Frequency

Population	CAF	p-value	Status
African	0.012	0.012	notable
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00038	0.00038	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.732
RVIS EVS: 0.18
RVIS percentile EVS: 66.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.305

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium