SEH1L
SEH1 like nucleoporin, the group of WD repeat domain containing|Nucleoporins|GATOR2 subcomplex
Basic information
Region (hg38): 18:12947132-12987536
Links
Phenotypes
GenCC
Source:
No genCC data.
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 SEH1L 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 | |||||
| missense | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 19 | 0 | 1 |
Variants in SEH1L
This is a list of pathogenic ClinVar variants found in the SEH1L region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-12948158-G-A | not specified | Uncertain significance (Oct 30, 2023) | ||
| 18-12951874-G-T | not specified | Uncertain significance (Jun 29, 2023) | ||
| 18-12963363-C-A | not specified | Uncertain significance (Oct 05, 2022) | ||
| 18-12971181-G-A | Tooth agenesis | Uncertain significance (-) | ||
| 18-12971206-A-G | not specified | Uncertain significance (Jul 13, 2021) | ||
| 18-12971216-C-T | Benign (Aug 16, 2018) | |||
| 18-12978778-T-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 18-12978804-A-G | not specified | Uncertain significance (Apr 25, 2023) | ||
| 18-12978816-C-G | not specified | Uncertain significance (Jan 06, 2023) | ||
| 18-12978861-G-T | not specified | Uncertain significance (Dec 11, 2023) | ||
| 18-12978888-G-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 18-12982538-G-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 18-12982582-A-T | not specified | Uncertain significance (Oct 25, 2023) | ||
| 18-12982622-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
| 18-12984138-G-C | not specified | Uncertain significance (Jun 30, 2022) | ||
| 18-12986873-C-T | not specified | Uncertain significance (May 27, 2022) | ||
| 18-12986891-G-C | not specified | Uncertain significance (Dec 06, 2022) | ||
| 18-12986918-C-G | not specified | Uncertain significance (Apr 22, 2022) | ||
| 18-12986941-C-T | not specified | Uncertain significance (Feb 28, 2024) | ||
| 18-12987005-G-A | not specified | Uncertain significance (Jul 17, 2023) | ||
| 18-12987038-C-T | not specified | Uncertain significance (May 30, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEH1L | protein_coding | protein_coding | ENST00000399892 | 9 | 40404 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.149 | 0.851 | 125718 | 0 | 30 | 125748 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.74 | 164 | 240 | 0.684 | 0.0000121 | 2765 |
| Missense in Polyphen | 31 | 70.196 | 0.44162 | 848 | ||
| Synonymous | 0.278 | 79 | 82.2 | 0.961 | 0.00000425 | 805 |
| Loss of Function | 3.33 | 6 | 23.4 | 0.257 | 0.00000135 | 240 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000240 | 0.000239 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000185 | 0.000185 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000656 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the Nup107-160 subcomplex of the nuclear pore complex (NPC). The Nup107-160 subcomplex is required for the assembly of a functional NPC. The Nup107-160 subcomplex is also required for normal kinetochore microtubule attachment, mitotic progression and chromosome segregation. This subunit plays a role in recruitment of the Nup107-160 subcomplex to the kinetochore. {ECO:0000269|PubMed:15146057, ECO:0000269|PubMed:17363900}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);tRNA processing;Disease;Signal Transduction;Gene expression (Transcription);Regulation of HSF1-mediated heat shock response;Metabolism of carbohydrates;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;snRNP Assembly;Vpr-mediated nuclear import of PICs;SUMOylation of DNA damage response and repair proteins;Transport of Ribonucleoproteins into the Host Nucleus;Viral Messenger RNA Synthesis;Export of Viral Ribonucleoproteins from Nucleus;SUMOylation of chromatin organization proteins;Influenza Viral RNA Transcription and Replication;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;NEP/NS2 Interacts with the Cellular Export Machinery;Metabolism of proteins;Influenza Life Cycle;Influenza Infection;Metabolism of RNA;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Infectious disease;Metabolism;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;RHO GTPases Activate Formins;SUMOylation;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;RHO GTPase Effectors;Signaling by Rho GTPases;Nuclear Pore Complex (NPC) Disassembly;tRNA processing in the nucleus;Transport of Mature mRNA derived from an Intron-Containing Transcript;Metabolism of non-coding RNA;Cellular response to heat stress;Nuclear Envelope Breakdown;Mitotic Prophase;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Resolution of Sister Chromatid Cohesion;Interactions of Vpr with host cellular proteins;Cell Cycle, Mitotic;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Gene Silencing by RNA
(Consensus)
Recessive Scores
- pRec
- 0.137
Intolerance Scores
- loftool
- 0.380
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 45.13
Haploinsufficiency Scores
- pHI
- 0.755
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.625
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.848
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Seh1l
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- cytokine production involved in inflammatory response;mRNA export from nucleus;nuclear pore organization;mitotic metaphase plate congression;viral process;positive regulation of TOR signaling;cellular response to amino acid starvation;cellular protein-containing complex localization;defense response to Gram-positive bacterium;cell division;attachment of mitotic spindle microtubules to kinetochore;positive regulation of TORC1 signaling
- Cellular component
- kinetochore;condensed chromosome kinetochore;nuclear envelope;lysosomal membrane;cytosol;nuclear pore outer ring;Seh1-associated complex;GATOR2 complex
- Molecular function
- protein binding