TMEM258

protein-coding

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

Gene summary

Predicted to enable oligosaccharyltransferase complex binding activity. Involved in protein N-linked glycosylation. Acts upstream of or within protein secretion and response to endoplasmic reticulum stress. Located in endoplasmic reticulum and membrane. Part of oligosaccharyltransferase complex A and oligosaccharyltransferase complex B. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C11orf10

MANE transcript

NM_014206.4

Inheritance

—

ClinVar variants

U:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr11:61,768,501-61,792,802

External References & Databases

Ensembl (ENSG00000134825)

Transcript & Mutation Effects

hg38 • Region Span ~24.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM258 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014206.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	0	0	9

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014206.4	RefSeq	NP_055021.1	3	MANE Select
ENST00000537328.6	Ensembl	ENSP00000443216.1	3	MANE Select
ENST00000257262.12	Ensembl	ENSP00000257262.8	3	Standard
ENST00000535297.1	Ensembl	ENSP00000437809.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein N-linked glycosylation

Cellular Component

endoplasmic reticulum
integral component of membrane
oligosaccharyltransferase I complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000537328
Coding exons: 3
Length: 24302
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125728
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.363	39	45.9	0.849	0.00000261	506
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E

Gene Damage Prediction

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