SERINC3

serine incorporator 3

Basic information

Region (hg38): 20:44496220-44522085

Previous symbols: [ "TDE1" ]

Links

ENSG00000132824 ∙ NCBI:10955 ∙ OMIM:607165 ∙ HGNC:11699 ∙ Uniprot:Q13530 ∙ 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 SERINC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERINC3 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						0
missense			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in SERINC3

This is a list of pathogenic ClinVar variants found in the SERINC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-44500302-G-C		not specified	Uncertain significance (Sep 27, 2022)
20-44500316-T-C		not specified	Uncertain significance (Jun 09, 2022)
20-44500354-A-G		not specified	Uncertain significance (Jan 20, 2023)
20-44500391-C-G		not specified	Uncertain significance (Sep 29, 2022)
20-44500404-G-C		not specified	Uncertain significance (Jun 30, 2022)
20-44501114-C-A		not specified	Uncertain significance (Mar 28, 2023)
20-44501139-G-T		not specified	Uncertain significance (Jun 17, 2022)
20-44501167-C-T		not specified	Uncertain significance (Jun 01, 2023)
20-44501208-C-T		not specified	Likely benign (Mar 11, 2024)
20-44501217-C-T		not specified	Likely benign (May 04, 2023)
20-44501242-C-T		not specified	Uncertain significance (Jul 08, 2022)
20-44503821-T-A		not specified	Uncertain significance (Dec 15, 2022)
20-44503896-G-A		not specified	Uncertain significance (Mar 19, 2024)
20-44504805-T-G		not specified	Uncertain significance (Dec 12, 2022)
20-44504857-G-C		not specified	Uncertain significance (Nov 06, 2023)
20-44504878-C-A		not specified	Uncertain significance (Dec 12, 2022)
20-44506853-T-C		not specified	Likely benign (Jun 01, 2023)
20-44506915-T-C		not specified	Uncertain significance (Mar 29, 2022)
20-44506953-G-C		not specified	Uncertain significance (Mar 29, 2023)
20-44506967-T-C		not specified	Uncertain significance (Nov 17, 2022)
20-44506969-T-C		not specified	Uncertain significance (Jun 24, 2022)
20-44506990-A-C		not specified	Uncertain significance (Dec 08, 2023)
20-44509905-C-A		not specified	Uncertain significance (Jun 17, 2024)
20-44510010-A-G		not specified	Uncertain significance (Feb 06, 2024)
20-44511309-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERINC3	protein_coding	protein_coding	ENST00000342374	10	25889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.779	0.221	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.162	258	265	0.972	0.0000139	3096
Missense in Polyphen		84	102.35	0.82075		1280
Synonymous	0.741	89	98.3	0.905	0.00000533	925
Loss of Function	3.62	4	22.6	0.177	0.00000111	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000331	0.000318
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000275	0.000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000727	0.0000653
Other	0.00	0.00

dbNSFP

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). {ECO:0000269|PubMed:26416733, ECO:0000269|PubMed:26416734}.
• Pathway: Metabolism of amino acids and derivatives;Metabolism;Amino acid synthesis and interconversion (transamination);Serine biosynthesis (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.747
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.530
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.774

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serinc3
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype

Gene ontology

• Biological process: L-serine biosynthetic process;phosphatidylserine metabolic process;sphingolipid metabolic process;detection of virus;L-serine transport;innate immune response;defense response to virus;positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
• Cellular component: Golgi membrane;plasma membrane;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: L-serine transmembrane transporter activity