SERINC2

serine incorporator 2

Basic information

Region (hg38): 1:31409565-31434680

Previous symbols: [ "TDE2L" ]

Links

ENSG00000168528 ∙ NCBI:347735 ∙ OMIM:614549 ∙ HGNC:23231 ∙ Uniprot:Q96SA4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SERINC2 gene.

• not_specified (89 variants)
• not_provided (6 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERINC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178865.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			86	6	1	93
nonsense						0
start loss						0
frameshift					1	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	86	7	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERINC2	protein_coding	protein_coding	ENST00000373710	11	25114

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.92e-13	0.0886	125511	0	237	125748	0.000943

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.262	315	302	1.04	0.0000196	3024
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0120	0.0120
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000383	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.000383	0.000381
South Asian	0.000196	0.000196
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of amino acids and derivatives;Metabolism;Amino acid synthesis and interconversion (transamination);Serine biosynthesis (Consensus)

Intolerance Scores

• loftool: 0.732
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.17

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.289
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.305

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serinc2

Gene ontology

• 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