SERINC5

protein-coding

serine incorporator 5

Gene summary

Enables phospholipid scramblase activity. Involved in antiviral innate immune response and plasma membrane phospholipid scrambling. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C5orf12

MANE transcript

NM_001174072.3

Inheritance

—

ClinVar variants

U:58B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr5:80,111,228-80,256,048

External References & Databases

Ensembl (ENSG00000164300)

Transcript & Mutation Effects

hg38 • Region Span ~144.8 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 SERINC5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001174072.3. 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	3 clinvar	3 clinvar	7
missense			55 clinvar	1 clinvar		56
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	58	4	3	65

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001174072.3	RefSeq	NP_001167543.1	12	MANE Select
ENST00000507668.7	Ensembl	ENSP00000426237.3	12	MANE Select
NM_001174071.3	RefSeq	NP_001167542.1	12	Standard
NM_178276.7	RefSeq	NP_840060.1	12	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
phospholipid biosynthetic process
detection of virus

Molecular Function

L-serine transmembrane transporter activity

Cellular Component

Golgi apparatus
plasma membrane
integral component of membrane
myelin sheath
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000512721
Coding exons: 12
Length: 144849
Individuals with no LoFs: 124620
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 124645
p: 0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.969	210	253	0.829	0.0000138	2983
Missense (PolyPhen)		65	107.22	0.60623		1343
Synonymous	-0.805	113	103	1.10	0.00000634	873
Loss of Function	2.50	13	27.0	0.481	0.00000149	308

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00017	0.00013	rare
Latino/Admixed American	0.000063	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000097	0.000093	rare
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.00011	0.000098	rare
Other	0.00050	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

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). Enhances the incorporation of serine into phosphatidylserine and sphingolipids. May play a role in providing serine molecules for the formation of myelin glycosphingolipids in oligodendrocytes (By similarity). {ECO:0000250|UniProtKB:Q63175, ECO:0000269|PubMed:26416733, ECO:0000269|PubMed:26416734}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

LoFtool: 0.870
RVIS EVS: -0.2
RVIS percentile EVS: 38.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.128

Gene Damage Prediction

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