SEZ6L
Basic information
Region (hg38): 22:26169461-26383597
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 7 | |||||
missense | 59 | 64 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 4 | |||||
Total | 0 | 0 | 62 | 7 | 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) | ||
22-26292604-C-G | not specified | Uncertain significance (May 30, 2024) | ||
22-26292616-T-C | not specified | Uncertain significance (Dec 06, 2021) | ||
22-26292634-G-A | not specified | Uncertain significance (Apr 12, 2024) | ||
22-26292655-C-G | not specified | Uncertain significance (Feb 13, 2023) | ||
22-26292684-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
22-26292811-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
22-26292840-G-A | not specified | Uncertain significance (Sep 14, 2023) | ||
22-26292845-G-T | not specified | Uncertain significance (Nov 17, 2023) | ||
22-26292846-G-A | not specified | Uncertain significance (May 08, 2024) | ||
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) | ||
22-26292978-G-A | not specified | Uncertain significance (Apr 06, 2024) | ||
22-26292984-G-T | not specified | Uncertain significance (Mar 01, 2023) | ||
22-26293005-G-T | not specified | Uncertain significance (May 26, 2022) |
GnomAD
Source:
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:
- 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
- Molecular function