TMEM259

transmembrane protein 259

Basic information

Region (hg38): 19:1009648-1021179

Previous symbols: [ "C19orf6" ]

Links

ENSG00000182087 ∙ NCBI:91304 ∙ OMIM:611011 ∙ HGNC:17039 ∙ Uniprot:Q4ZIN3 ∙ 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 TMEM259 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM259 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		1
missense			72	3		75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	72	4	0

Variants in TMEM259

This is a list of pathogenic ClinVar variants found in the TMEM259 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-1010388-T-C		not specified	Uncertain significance (Nov 13, 2024)
19-1010456-G-A		not specified	Uncertain significance (Jan 21, 2025)
19-1010456-G-T		not specified	Uncertain significance (Aug 01, 2024)
19-1010490-C-T		not specified	Uncertain significance (Mar 20, 2023)
19-1010495-G-A		not specified	Uncertain significance (Apr 16, 2024)
19-1010504-A-G		not specified	Uncertain significance (Dec 16, 2023)
19-1010507-G-A		not specified	Uncertain significance (Aug 01, 2024)
19-1010532-G-A		not specified	Uncertain significance (Feb 01, 2023)
19-1010544-G-C		not specified	Uncertain significance (Jul 20, 2022)
19-1010562-C-T		not specified	Uncertain significance (Aug 02, 2022)
19-1010610-C-T		not specified	Likely benign (Jan 23, 2024)
19-1010637-C-T		not specified	Uncertain significance (Mar 01, 2025)
19-1010639-G-A		not specified	Uncertain significance (Dec 04, 2024)
19-1010660-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-1010676-G-A		not specified	Uncertain significance (Nov 29, 2023)
19-1010682-C-T		not specified	Uncertain significance (Nov 07, 2023)
19-1010691-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-1010700-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-1010715-G-T		not specified	Uncertain significance (Aug 11, 2022)
19-1010718-G-A		not specified	Uncertain significance (Feb 19, 2025)
19-1010747-G-A		not specified	Uncertain significance (Oct 14, 2023)
19-1010747-G-C		not specified	Uncertain significance (Sep 30, 2024)
19-1010750-G-A		not specified	Uncertain significance (Jun 06, 2023)
19-1010783-G-A		not specified	Likely benign (Sep 20, 2023)
19-1010783-G-T		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM259	protein_coding	protein_coding	ENST00000356663	11	11471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00592	123874	0	3	123877	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	296	365	0.812	0.0000245	3919
Missense in Polyphen		83	138.17	0.60071		1440
Synonymous	-2.48	211	170	1.24	0.0000135	1250
Loss of Function	3.90	1	19.7	0.0509	8.38e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000297	0.0000269
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role in the ERAD pathway required for clearance of misfolded proteins in the endoplasmic reticulum (ER). Promotes survival of motor neurons, probably by protecting against ER stress. {ECO:0000250|UniProtKB:Q8CIV2}.

Haploinsufficiency Scores

• pHI: 0.265
• hipred: Y
• hipred_score: 0.673
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem259
• Phenotype: normal phenotype

Gene ontology

• Biological process: response to endoplasmic reticulum stress;negative regulation of neuron death;positive regulation of ERAD pathway
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane