TMEM69

transmembrane protein 69

Basic information

Region (hg38): 1:45688181-45694436

Previous symbols: [ "C1orf154" ]

Links

ENSG00000159596 ∙ NCBI:51249 ∙ ∙ HGNC:28035 ∙ Uniprot:Q5SWH9 ∙ 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 TMEM69 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM69 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in TMEM69

This is a list of pathogenic ClinVar variants found in the TMEM69 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-45693259-C-G		not specified	Uncertain significance (Dec 20, 2023)
1-45693274-T-C		not specified	Uncertain significance (Nov 17, 2022)
1-45693309-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-45693427-A-C		not specified	Uncertain significance (Jun 02, 2023)
1-45693451-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-45693486-G-A		not specified	Likely benign (Oct 25, 2022)
1-45693501-G-T		not specified	Uncertain significance (Dec 20, 2023)
1-45693523-A-G		not specified	Uncertain significance (Feb 05, 2024)
1-45693529-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-45693636-T-C		not specified	Uncertain significance (Jul 26, 2021)
1-45693660-G-T		not specified	Uncertain significance (Jul 20, 2022)
1-45693661-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-45693778-A-C		not specified	Uncertain significance (Jun 29, 2023)
1-45693793-T-A		not specified	Uncertain significance (Jul 09, 2021)
1-45693861-A-T		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM69	protein_coding	protein_coding	ENST00000372025	2	7230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000187	0.487	124693	0	101	124794	0.000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.203	120	126	0.949	0.00000561	1600
Missense in Polyphen		24	33.925	0.70744		455
Synonymous	1.40	32	43.8	0.731	0.00000187	510
Loss of Function	0.342	6	6.97	0.860	2.93e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000756	0.000755
Ashkenazi Jewish	0.00367	0.00368
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000195	0.000194
Middle Eastern	0.0000556	0.0000556
South Asian	0.000817	0.000817
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.525
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.0586
• hipred: N
• hipred_score: 0.123
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.474

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem69

Gene ontology

• Cellular component: integral component of membrane