TMEM258
Basic information
Region (hg38): 11:61768500-61792802
Previous symbols: [ "C11orf10" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM258 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 | 0 | |||||
missense | 2 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 2 | 0 | 0 |
Variants in TMEM258
This is a list of pathogenic ClinVar variants found in the TMEM258 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-61769111-G-A | Benign (May 13, 2021) | |||
11-61769256-G-A | MYRF-related disorder | Likely benign (Oct 18, 2021) | ||
11-61769263-A-G | MYRF-related disorder | Likely benign (Oct 04, 2022) | ||
11-61769286-C-G | not specified | Uncertain significance (Jan 09, 2020) | ||
11-61769286-CG-C | Cardiac-urogenital syndrome | Pathogenic (Jul 01, 2022) | ||
11-61769290-C-A | Likely benign (Apr 01, 2022) | |||
11-61770057-T-G | Benign (May 13, 2021) | |||
11-61770218-G-A | Benign (May 14, 2021) | |||
11-61770248-C-T | Encephalitis/encephalopathy, mild, with reversible myelin vacuolization | Uncertain significance (Aug 12, 2019) | ||
11-61770260-C-T | Inborn genetic diseases | Uncertain significance (Mar 22, 2023) | ||
11-61770274-TGA-T | MYRF-related disorder | Pathogenic (May 17, 2023) | ||
11-61770290-G-A | Inborn genetic diseases | Uncertain significance (Mar 02, 2023) | ||
11-61770305-C-T | MYRF-related disorder | Uncertain significance (Aug 29, 2022) | ||
11-61770306-G-A | MYRF-related disorder | Likely benign (Jul 11, 2022) | ||
11-61770318-C-T | Inborn genetic diseases | Uncertain significance (Jan 03, 2022) | ||
11-61770352-G-C | MYRF-related disorder | Likely benign (Dec 26, 2020) | ||
11-61770355-A-C | MYRF-related disorder | Likely benign (Jan 28, 2023) | ||
11-61770356-C-T | Inborn genetic diseases | Uncertain significance (Apr 12, 2022) | ||
11-61770365-C-T | Inborn genetic diseases | Uncertain significance (Dec 27, 2023) | ||
11-61770392-C-T | Inborn genetic diseases | Uncertain significance (Nov 08, 2021) | ||
11-61770405-T-C | MYRF-related disorder | Likely benign (Apr 15, 2022) | ||
11-61770423-TC-T | Cardiac-urogenital syndrome | Likely pathogenic (Jan 04, 2022) | ||
11-61770433-C-A | Cardiac-urogenital syndrome | Pathogenic (Dec 21, 2020) | ||
11-61770438-C-T | Inborn genetic diseases | Uncertain significance (May 24, 2023) | ||
11-61770486-C-T | MYRF-related disorder | Benign (Sep 09, 2019) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TMEM258 | protein_coding | protein_coding | ENST00000537328 | 3 | 24302 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00185 | 0.501 | 125722 | 0 | 6 | 125728 | 0.0000239 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.363 | 39 | 45.9 | 0.849 | 0.00000261 | 506 |
Missense in Polyphen | 5 | 5.4477 | 0.91781 | 89 | ||
Synonymous | 0.138 | 18 | 18.8 | 0.959 | 0.00000123 | 160 |
Loss of Function | 0.0965 | 4 | 4.21 | 0.949 | 1.79e-7 | 51 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000442 | 0.0000440 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as component of the N-oligosaccharyl transferase (OST) complex which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains. Required for full OST catalytic activity in N-glycosylation (PubMed:26472760, PubMed:27974209). Involved in endoplasmic reticulum (ER) homeostasis in the colonic epithelium (By similarity). {ECO:0000250|UniProtKB:P61166, ECO:0000269|PubMed:26472760, ECO:0000269|PubMed:27974209}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.25
Haploinsufficiency Scores
- pHI
- 0.255
- hipred
- N
- hipred_score
- 0.250
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Low | Low | Low |
Primary Immunodeficiency | Medium | Low | Medium |
Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Tmem258
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular 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); immune system phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- protein N-linked glycosylation
- Cellular component
- endoplasmic reticulum;integral component of membrane;oligosaccharyltransferase I complex
- Molecular function