SERINC1

serine incorporator 1

Basic information

Region (hg38): 6:122443351-122471807

Previous symbols: [ "TDE2" ]

Links

ENSG00000111897 ∙ NCBI:57515 ∙ OMIM:614548 ∙ HGNC:13464 ∙ Uniprot:Q9NRX5 ∙ 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 SERINC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERINC1 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding						0
Total	0	0	16	0	0

Variants in SERINC1

This is a list of pathogenic ClinVar variants found in the SERINC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-122445136-A-C		not specified	Uncertain significance (Apr 20, 2024)
6-122445166-G-T		not specified	Uncertain significance (Oct 25, 2023)
6-122446783-T-C		not specified	Uncertain significance (Oct 26, 2021)
6-122446792-G-A		not specified	Uncertain significance (Oct 29, 2021)
6-122446829-A-G		not specified	Uncertain significance (Aug 26, 2024)
6-122446893-G-A		not specified	Likely benign (May 29, 2024)
6-122446925-C-T		not specified	Uncertain significance (Dec 16, 2022)
6-122447000-G-A		not specified	Uncertain significance (Sep 30, 2024)
6-122447004-G-A			Likely benign (Mar 01, 2024)
6-122447139-A-C		not specified	Uncertain significance (Oct 27, 2022)
6-122447149-G-T		not specified	Uncertain significance (Oct 25, 2024)
6-122447170-G-T		not specified	Uncertain significance (Feb 10, 2022)
6-122447201-C-G		not specified	Uncertain significance (Apr 18, 2023)
6-122447203-T-C		not specified	Uncertain significance (Sep 10, 2024)
6-122451758-C-CAAAAAAA			Likely benign (May 01, 2022)
6-122451991-T-G		not specified	Uncertain significance (Apr 25, 2022)
6-122451992-A-G		not specified	Uncertain significance (Jul 06, 2024)
6-122452007-C-T		not specified	Uncertain significance (Jun 01, 2023)
6-122453767-T-C			Likely benign (May 01, 2023)
6-122453903-C-G		not specified	Uncertain significance (Aug 02, 2021)
6-122456522-T-G		not specified	Uncertain significance (Jul 30, 2024)
6-122456577-C-T		not specified	Uncertain significance (Nov 22, 2023)
6-122456595-C-A		not specified	Uncertain significance (Dec 19, 2022)
6-122458563-G-A		not specified	Uncertain significance (Apr 08, 2024)
6-122458567-C-T		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERINC1	protein_coding	protein_coding	ENST00000339697	10	28469

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00746	0.992	125718	0	18	125736	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	176	234	0.751	0.0000115	2942
Missense in Polyphen		50	85.253	0.58649		1154
Synonymous	-0.180	85	82.9	1.03	0.00000430	863
Loss of Function	3.00	8	23.8	0.337	0.00000117	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000125
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.000220	0.000217
South Asian	0.0000654	0.0000653
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances the incorporation of serine into phosphatidylserine and sphingolipids. {ECO:0000250|UniProtKB:Q7TNK0}.
• Pathway: Sphingolipid Metabolism;Metabolism of amino acids and derivatives;Metabolism;Amino acid synthesis and interconversion (transamination);Serine biosynthesis (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• pHI: 0.781
• hipred: N
• hipred_score: 0.492
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.415

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serinc1
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: phosphatidylserine metabolic process;sphingolipid metabolic process;phospholipid biosynthetic process;membrane biogenesis;positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity;positive regulation of serine C-palmitoyltransferase activity
• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: protein binding;enzyme binding;protein binding, bridging