SEZ6L2

seizure related 6 homolog like 2, the group of Sushi domain containing

Basic information

Region (hg38): 16:29871159-29899550

Links

ENSG00000174938 ∙ NCBI:26470 ∙ OMIM:616667 ∙ HGNC:30844 ∙ Uniprot:Q6UXD5 ∙ 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 SEZ6L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEZ6L2 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				7	7	14
missense			41	4	2	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	11	9

Variants in SEZ6L2

This is a list of pathogenic ClinVar variants found in the SEZ6L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-29872264-A-T		not specified	Uncertain significance (Jun 14, 2023)
16-29872437-C-T		not specified	Uncertain significance (Jan 27, 2022)
16-29872446-T-C		not specified	Uncertain significance (Jan 22, 2024)
16-29872455-C-T		not specified	Uncertain significance (Aug 07, 2023)
16-29872480-C-G			Likely benign (Dec 31, 2019)
16-29873306-C-T		not specified	Uncertain significance (Jul 15, 2021)
16-29873406-C-T			Benign (Dec 31, 2019)
16-29873426-A-G		not specified	Uncertain significance (May 04, 2023)
16-29873586-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-29873724-T-G		not specified	Uncertain significance (Apr 25, 2023)
16-29873726-A-G		not specified	Uncertain significance (Dec 28, 2022)
16-29876761-T-A		not specified	Uncertain significance (Apr 12, 2024)
16-29876927-G-A		not specified	Uncertain significance (Dec 09, 2023)
16-29877325-G-A		not specified	Uncertain significance (May 24, 2023)
16-29877378-G-A		not specified	Uncertain significance (May 14, 2024)
16-29877408-C-T		not specified	Uncertain significance (Jun 16, 2024)
16-29877420-C-T		not specified	Uncertain significance (Oct 06, 2023)
16-29877424-C-T		not specified	Uncertain significance (Jun 21, 2023)
16-29877442-G-C		not specified	Uncertain significance (Dec 07, 2021)
16-29878404-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-29878411-C-T		not specified	Uncertain significance (Aug 02, 2021)
16-29879905-G-A		not specified	Uncertain significance (Jun 21, 2022)
16-29885668-G-A			Benign (Jun 13, 2018)
16-29885674-C-G			Likely benign (May 25, 2018)
16-29885675-C-T		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEZ6L2	protein_coding	protein_coding	ENST00000308713	17	28389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.117	0.883	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.75	452	570	0.793	0.0000349	5735
Missense in Polyphen		132	194.11	0.68004		2048
Synonymous	0.238	259	264	0.981	0.0000177	2000
Loss of Function	4.42	10	40.3	0.248	0.00000187	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000158	0.000154
Ashkenazi Jewish	0.000111	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000137	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.0000686	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.607
• rvis_EVS: -1.12
• rvis_percentile_EVS: 6.58

Haploinsufficiency Scores

• pHI: 0.535
• hipred: Y
• hipred_score: 0.630
• ghis: 0.656

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.461

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sez6l2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal 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)

Zebrafish Information Network

• Gene name: sez6l2
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of membrane