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.

• not_specified (45 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_000020755.4. 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				2		2
missense			44			44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	2	0

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