SEZ6L

seizure related 6 homolog like, the group of Sushi domain containing

Basic information

Region (hg38): 22:26169461-26383597

Links

ENSG00000100095 ∙ NCBI:23544 ∙ OMIM:607021 ∙ HGNC:10763 ∙ Uniprot:Q9BYH1 ∙ 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 SEZ6L gene.

• Inborn genetic diseases (40 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEZ6L 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				3	4	7
missense			37	2	2	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2	1		3
Total	0	0	39	6	6

Variants in SEZ6L

This is a list of pathogenic ClinVar variants found in the SEZ6L region.

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

Position	Type	Phenotype	Significance	ClinVar
22-26169677-C-T		not specified	Uncertain significance (Dec 27, 2023)
22-26169685-C-A		not specified	Uncertain significance (Oct 22, 2021)
22-26169713-C-G		not specified	Uncertain significance (Sep 13, 2023)
22-26292417-G-A		not specified	Uncertain significance (Nov 17, 2023)
22-26292517-C-T		not specified	Uncertain significance (Mar 29, 2022)
22-26292518-G-A			Likely benign (Jun 18, 2018)
22-26292573-A-G		not specified	Uncertain significance (Apr 13, 2023)
22-26292580-C-T		not specified	Uncertain significance (May 25, 2022)
22-26292593-C-G		not specified	Uncertain significance (Jul 19, 2022)
22-26292594-G-A		not specified	Uncertain significance (Jan 02, 2024)
22-26292616-T-C		not specified	Uncertain significance (Dec 06, 2021)
22-26292655-C-G		not specified	Uncertain significance (Feb 13, 2023)
22-26292684-G-A		not specified	Uncertain significance (Jan 26, 2022)
22-26292840-G-A		not specified	Uncertain significance (Sep 14, 2023)
22-26292845-G-T		not specified	Uncertain significance (Nov 17, 2023)
22-26292892-C-G		not specified	Uncertain significance (Mar 14, 2024)
22-26292898-C-G		not specified	Uncertain significance (Feb 27, 2024)
22-26292903-G-A		not specified	Uncertain significance (Dec 16, 2023)
22-26292984-G-T		not specified	Uncertain significance (Mar 01, 2023)
22-26293005-G-T		not specified	Uncertain significance (May 26, 2022)
22-26293038-A-T		not specified	Uncertain significance (Mar 06, 2023)
22-26293065-G-A		not specified	Uncertain significance (Feb 23, 2023)
22-26293087-A-G		not specified	Uncertain significance (May 08, 2023)
22-26293089-G-T		Malignant tumor of prostate	Uncertain significance (-)
22-26293134-G-A		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEZ6L	protein_coding	protein_coding	ENST00000248933	17	214123

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.507	0.493	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	495	596	0.831	0.0000349	6598
Missense in Polyphen		148	249.25	0.59379		2771
Synonymous	-0.0901	273	271	1.01	0.0000188	2105
Loss of Function	4.90	10	45.7	0.219	0.00000230	526

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May contribute to specialized endoplasmic reticulum functions in neurons. {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.331
• rvis_EVS: -2.03
• rvis_percentile_EVS: 1.69

Haploinsufficiency Scores

• pHI: 0.301
• hipred: N
• hipred_score: 0.489
• ghis: 0.617

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.295

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sez6l
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: adult locomotory behavior;cerebellar Purkinje cell layer development;synapse maturation;regulation of protein kinase C signaling
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;neuronal cell body