SERINC4

protein-coding

serine incorporator 4

Gene summary

Predicted to be involved in phospholipid biosynthetic process. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001258031.2

Inheritance

—

ClinVar variants

U:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.03

Max pathogenic AF

—

Genomic locus

chr15:43,794,162-43,800,220

External References & Databases

Ensembl (ENSG00000184716)

Transcript & Mutation Effects

hg38 • Region Span ~6.1 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 SERINC4 variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001258031.2. 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						0
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	4	0	0	4

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001258031.2	RefSeq	NP_001244960.1	12	MANE Select
ENST00000319327.7	Ensembl	ENSP00000319796.6	12	MANE Select
NM_001258032.2	RefSeq	NP_001244961.1	8	Standard
ENST00000299969.10	Ensembl	ENSP00000299969.6	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

phospholipid biosynthetic process

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319327
Coding exons: 12
Length: 6060
Individuals with no LoFs: 125640
Homozygous LoFs: 0
Heterozygous LoFs: 108
Defined: 125748
p: 0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.444	302	281	1.07	0.0000147	3331
Missense (PolyPhen)		83	90.693	0.91518		1212
Synonymous	0.158	109	111	0.981	0.00000550	1081
Loss of Function	-0.155	26	25.2	1.03	0.00000116	285

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00075	0.00075	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00071	0.00065	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00054	0.00054	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Incorporates a polar amino acid serine into membranes and facilitates the synthesis of two serine-derived lipids, phosphatidylserine and sphingolipids. {ECO:0000269|PubMed:16120614}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.270

Gene Damage Prediction

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