TMEM258

transmembrane protein 258, the group of Oligosaccharyltransferase complex subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 11:61768501-61792802

Previous symbols: [ "C11orf10" ]

Links

ENSG00000134825 ∙ NCBI:746 ∙ OMIM:617615 ∙ HGNC:1164 ∙ Uniprot:P61165 ∙ 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 TMEM258 gene.

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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	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)
11-61769301-A-G		Inborn genetic diseases	Uncertain significance (Aug 27, 2024)
11-61769309-C-T		Cardiac-urogenital syndrome	Likely pathogenic (Sep 22, 2024)
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)
11-61770270-C-T		Inborn genetic diseases	Uncertain significance (Jun 07, 2024)
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 • Inborn genetic diseases	Uncertain significance (Mar 19, 2024)
11-61770306-G-A		MYRF-related disorder	Likely benign (Jul 11, 2022)
11-61770318-C-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
11-61770347-C-T		Inborn genetic diseases	Uncertain significance (May 13, 2024)
11-61770350-C-T			Uncertain significance (Nov 01, 2023)
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, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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 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