SEZ6

seizure related 6 homolog, the group of Sushi domain containing

Basic information

Region (hg38): 17:28954900-29006440

Links

ENSG00000063015 ∙ NCBI:124925 ∙ OMIM:616666 ∙ HGNC:15955 ∙ Uniprot:Q53EL9 ∙ 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 SEZ6 gene.

• Inborn genetic diseases (32 variants)
• not provided (13 variants)
• Childhood-onset schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEZ6 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				1	2	3
missense			29	5	7	41
nonsense						0
start loss						0
frameshift						0
inframe indel		1				1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	1	29	6	10

Variants in SEZ6

This is a list of pathogenic ClinVar variants found in the SEZ6 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28956196-A-G		not specified	Uncertain significance (Jan 26, 2023)
17-28956218-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-28956229-C-T		not specified	Uncertain significance (Dec 28, 2023)
17-28956230-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-28956432-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-28956438-G-C		not specified	Uncertain significance (Jul 05, 2023)
17-28956734-T-C		not specified	Likely benign (Jan 31, 2022)
17-28957076-A-G			Benign (Jul 11, 2017)
17-28957176-T-C			Benign (Dec 31, 2019)
17-28957191-C-T		not specified	Likely benign (Jun 22, 2021)
17-28957350-A-C		not specified	Uncertain significance (Jan 03, 2024)
17-28957425-A-G			Benign (Feb 02, 2021)
17-28957485-C-T		not specified	Uncertain significance (Nov 01, 2022)
17-28957500-C-T		not specified	Uncertain significance (Nov 21, 2023)
17-28957548-AG-A			Benign (Feb 02, 2021)
17-28957966-G-T		not specified	Uncertain significance (Apr 13, 2023)
17-28957984-G-C		not specified	Uncertain significance (Apr 19, 2023)
17-28958117-G-A		not specified	Uncertain significance (Jun 29, 2022)
17-28958132-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-28958133-G-A		not specified	Uncertain significance (Sep 26, 2023)
17-28959040-C-T		Nonsyndromic hearing impairment	Uncertain significance (-)
17-28959135-C-T			Benign (Dec 31, 2019)
17-28959337-C-T		not specified	Uncertain significance (Jan 04, 2024)
17-28959404-C-T			Benign (Dec 31, 2018)
17-28959444-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEZ6	protein_coding	protein_coding	ENST00000317338	17	51540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000175	1.00	124740	0	38	124778	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	449	582	0.771	0.0000331	6347
Missense in Polyphen		129	224.43	0.57479		2405
Synonymous	1.20	214	238	0.901	0.0000142	2068
Loss of Function	3.78	18	45.5	0.396	0.00000248	470

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000428	0.000422
Ashkenazi Jewish	0.0000997	0.0000994
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000163	0.000159
Middle Eastern	0.000111	0.000111
South Asian	0.000171	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cell-cell recognition and in neuronal membrane signaling. Seems to be important for the achievement of the necessary balance between dendrite elongation and branching during the elaboration of a complex dendritic arbor. Involved in the development of appropriate excitatory synaptic connectivity (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0903

Intolerance Scores

• loftool: 0.936
• rvis_EVS: 1.25
• rvis_percentile_EVS: 93.47

Haploinsufficiency Scores

• pHI: 0.369
• hipred: N
• hipred_score: 0.428
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.197

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sez6
• 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); normal phenotype; 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;regulation of dendrite development;synapse maturation;excitatory postsynaptic potential;regulation of protein kinase C signaling
• Cellular component: endoplasmic reticulum;plasma membrane;integral component of membrane;neuronal cell body;dendritic spine;dendritic shaft;perinuclear region of cytoplasm;apical dendrite