TMEM169

transmembrane protein 169

Basic information

Region (hg38): 2:216081866-216102783

Links

ENSG00000163449 ∙ NCBI:92691 ∙ ∙ HGNC:25130 ∙ Uniprot:Q96HH4 ∙ 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 TMEM169 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM169 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	0

Variants in TMEM169

This is a list of pathogenic ClinVar variants found in the TMEM169 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-216096014-C-A		not specified	Uncertain significance (Sep 12, 2023)
2-216096036-G-A		not specified	Uncertain significance (Aug 14, 2023)
2-216096052-C-T		not specified	Uncertain significance (Mar 29, 2023)
2-216096078-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-216096082-G-A		not specified	Uncertain significance (Jun 01, 2023)
2-216096129-C-G		not specified	Uncertain significance (Mar 20, 2023)
2-216096130-G-T		not specified	Uncertain significance (Nov 22, 2021)
2-216096162-G-A		not specified	Uncertain significance (Apr 25, 2022)
2-216096228-G-A		not specified	Uncertain significance (Mar 02, 2023)
2-216099943-A-G		not specified	Uncertain significance (Mar 01, 2023)
2-216099977-G-A		not specified	Uncertain significance (Oct 03, 2022)
2-216099986-A-G		not specified	Uncertain significance (Mar 23, 2022)
2-216100084-G-A		not specified	Uncertain significance (Jul 12, 2022)
2-216100092-G-C		not specified	Uncertain significance (Apr 12, 2024)
2-216100093-G-C		not specified	Uncertain significance (Nov 03, 2022)
2-216100139-C-A		not specified	Uncertain significance (Jul 06, 2021)
2-216100291-C-T		not specified	Uncertain significance (Apr 05, 2023)
2-216100294-G-T		not specified	Uncertain significance (Nov 30, 2022)
2-216100302-C-G		not specified	Uncertain significance (Nov 21, 2022)
2-216100352-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-216100377-A-T		not specified	Uncertain significance (Jun 22, 2021)
2-216100387-G-A		not specified	Uncertain significance (Dec 17, 2023)
2-216100390-A-G		not specified	Uncertain significance (Jul 20, 2021)
2-216100396-A-G		not specified	Uncertain significance (Jan 23, 2023)
2-216100400-G-C		not specified	Uncertain significance (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM169	protein_coding	protein_coding	ENST00000454545	2	20918

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0118	0.954	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.299	156	167	0.935	0.00000948	1928
Missense in Polyphen		58	61.697	0.94008		776
Synonymous	-0.215	70	67.8	1.03	0.00000424	591
Loss of Function	1.84	5	11.8	0.422	6.11e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000799	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.0708
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.0851
• hipred: N
• hipred_score: 0.333
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.588

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem169

Gene ontology

• Cellular component: integral component of membrane