TMEM170A

transmembrane protein 170A

Basic information

Region (hg38): 16:75443054-75465497

Previous symbols: [ "TMEM170" ]

Links

ENSG00000166822 ∙ NCBI:124491 ∙ ∙ HGNC:29577 ∙ Uniprot:Q8WVE7 ∙ 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 TMEM170A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM170A 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in TMEM170A

This is a list of pathogenic ClinVar variants found in the TMEM170A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-75447577-C-G		not specified	Uncertain significance (Jun 28, 2022)
16-75451725-G-T		not specified	Uncertain significance (Feb 05, 2024)
16-75451743-T-C		not specified	Uncertain significance (Dec 13, 2022)
16-75451798-G-C		not specified	Uncertain significance (Mar 31, 2023)
16-75464498-G-C		not specified	Uncertain significance (Jan 27, 2022)
16-75464504-G-C		not specified	Uncertain significance (May 27, 2022)
16-75464510-C-T		not specified	Uncertain significance (Oct 26, 2021)
16-75464551-T-C		not specified	Uncertain significance (Mar 15, 2024)
16-75464582-C-T		not specified	Uncertain significance (May 08, 2024)
16-75464594-G-A		not specified	Uncertain significance (Feb 07, 2023)
16-75464597-C-T		not specified	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM170A	protein_coding	protein_coding	ENST00000561878	3	22444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.72e-7	0.0759	125564	0	184	125748	0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.505	90	77.5	1.16	0.00000380	897
Missense in Polyphen		37	35.671	1.0373		419
Synonymous	-2.64	52	32.8	1.59	0.00000160	323
Loss of Function	-1.09	8	5.28	1.51	3.09e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000611	0.000544
Finnish	0.000878	0.000878
European (Non-Finnish)	0.000689	0.000686
Middle Eastern	0.000611	0.000544
South Asian	0.00205	0.00203
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a regulator of endoplasmic reticulum (ER) and nuclear envelope (NE) morphogenesis. Affects the ratio between tubular ER and ER sheets by promoting sheet formation at the expense of tubules. Influences NE expansion, nuclear pore complex formation and proper localization of inner nuclear membrane proteins (PubMed:26906412). {ECO:0000269|PubMed:26906412}.

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.240
• hipred: N
• hipred_score: 0.112
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.353

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem170

Gene ontology

• Biological process: nuclear envelope organization;nuclear pore complex assembly;endoplasmic reticulum tubular network organization
• Cellular component: nuclear envelope;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein binding