SEZ6

seizure related 6 homolog, the group of Sushi domain containing

Basic information

Region (hg38): 17:28954901-29006440

Links

ENSG00000063015 ∙ NCBI:124925 ∙ OMIM:616666 ∙ HGNC:15955 ∙ Uniprot:Q53EL9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 13.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_178860.5	NP_849191.3	17	yes	-
ENST00000317338.17	ENSP00000312942.11	17	yes	-
NM_001098635.2	NP_001092105.1	17	-	-
NM_001290202.2	NP_001277131.1	16	-	-

Phenotypes

GenCC

Source: genCC

• nonsyndromic genetic hearing loss (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEZ6 gene.

• not_specified (120 variants)
• not_provided (11 variants)
• Childhood-onset_schizophrenia (1 variants)
• Nonsyndromic_hearing_impairment (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. These statistics are base on transcript: NM_178860.5. 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				1	2	3
missense			116	8	6	130
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	116	9	8

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
		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

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

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