SERINC5

serine incorporator 5

Basic information

Region (hg38): 5:80111228-80256048

Previous symbols: [ "C5orf12" ]

Links

ENSG00000164300 ∙ NCBI:256987 ∙ OMIM:614551 ∙ HGNC:18825 ∙ Uniprot:Q86VE9 ∙ 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 SERINC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERINC5 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				4	3	7
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	30	4	4

Variants in SERINC5

This is a list of pathogenic ClinVar variants found in the SERINC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-80113607-C-T			Likely benign (Nov 01, 2022)
5-80143668-C-T		not specified	Uncertain significance (Oct 27, 2023)
5-80143670-G-C		not specified	Uncertain significance (Feb 24, 2025)
5-80143682-G-A		not specified	Uncertain significance (Apr 19, 2024)
5-80143684-G-A			Likely benign (Dec 01, 2022)
5-80143701-C-T		not specified	Uncertain significance (Aug 16, 2021)
5-80143776-C-T		not specified	Uncertain significance (Jul 02, 2024)
5-80143797-T-C		not specified	Uncertain significance (May 12, 2024)
5-80146106-C-T		not specified	Uncertain significance (Jun 16, 2023)
5-80146107-G-A			Benign (Jun 10, 2018)
5-80146136-A-G		not specified	Uncertain significance (Sep 02, 2024)
5-80146143-G-T		not specified	Uncertain significance (Aug 28, 2023)
5-80146231-G-T		not specified	Uncertain significance (Dec 05, 2024)
5-80147283-A-G		not specified	Uncertain significance (May 04, 2023)
5-80150917-C-T		not specified	Uncertain significance (Dec 18, 2023)
5-80150928-G-A		not specified	Uncertain significance (Dec 21, 2022)
5-80158867-T-C		not specified	Uncertain significance (Mar 19, 2024)
5-80158900-T-G			Likely benign (Mar 01, 2023)
5-80158939-C-G		not specified	Uncertain significance (Mar 11, 2022)
5-80158940-A-G			Benign (Feb 20, 2018)
5-80166446-C-T		not specified	Uncertain significance (Oct 11, 2024)
5-80166466-G-A		not specified	Uncertain significance (Nov 09, 2021)
5-80169343-A-G		not specified	Uncertain significance (Mar 01, 2023)
5-80169352-G-A		not specified	Uncertain significance (Feb 01, 2025)
5-80169374-G-C		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERINC5	protein_coding	protein_coding	ENST00000512721	12	144849

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000664	0.995	124620	0	25	124645	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.969	210	253	0.829	0.0000138	2983
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000233	0.000192
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.0000557	0.0000556
Finnish	0.0000968	0.0000928
European (Non-Finnish)	0.000102	0.0000973
Middle Eastern	0.0000557	0.0000556
South Asian	0.000105	0.0000980
Other	0.000497	0.000496

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

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.870
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.454
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serinc5

Gene ontology

• Biological process: L-serine biosynthetic process;phosphatidylserine metabolic process;sphingolipid metabolic process;phospholipid biosynthetic process;detection of virus;L-serine transport;viral process;myelination;innate immune response;defense response to virus;positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity;positive regulation of serine C-palmitoyltransferase activity
• Cellular component: Golgi apparatus;plasma membrane;integral component of membrane;myelin sheath;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: L-serine transmembrane transporter activity