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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			45	4	1	50
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	5	3

Variants in SERINC2

This is a list of pathogenic ClinVar variants found in the SERINC2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-31423768-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
1-31423834-G-A		not specified	Uncertain significance (Feb 10, 2023)
1-31424687-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-31424690-G-C		not specified	Uncertain significance (Dec 14, 2021)
1-31424705-G-A		not specified	Uncertain significance (May 15, 2023)
1-31424709-C-T			Benign (Jul 06, 2018)
1-31424722-G-A		not specified	Likely benign (Aug 15, 2023)
1-31424740-G-A			Benign (Dec 31, 2019)
1-31424762-A-G		not specified	Uncertain significance (Apr 08, 2022)
1-31424765-G-A		not specified	Uncertain significance (Jan 29, 2024)
1-31424776-C-T		not specified	Uncertain significance (Oct 16, 2023)
1-31424777-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-31424807-T-C		not specified	Uncertain significance (Feb 10, 2022)
1-31424825-T-C		not specified	Uncertain significance (Jun 10, 2021)
1-31424828-T-A		not specified	Uncertain significance (Jun 10, 2021)
1-31424830-T-A		not specified	Uncertain significance (Jun 10, 2021)
1-31424833-G-A		not specified	Uncertain significance (Jun 10, 2021)
1-31424845-C-G			Likely benign (Nov 01, 2022)
1-31424845-C-T			Likely benign (Jul 01, 2022)
1-31424854-C-T		not specified	Uncertain significance (Jun 05, 2023)
1-31424863-A-T		not specified	Uncertain significance (Jun 13, 2022)
1-31425370-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-31425374-G-A		not specified	Uncertain significance (Jan 31, 2024)
1-31425394-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-31425850-C-T		not specified	Uncertain significance (Mar 04, 2024)

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