TMEM170B

transmembrane protein 170B

Basic information

Region (hg38): 6:11537749-11583524

Links

ENSG00000205269 ∙ NCBI:100113407 ∙ ∙ HGNC:34244 ∙ Uniprot:Q5T4T1 ∙ 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 TMEM170B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM170B 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in TMEM170B

This is a list of pathogenic ClinVar variants found in the TMEM170B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-11538320-G-C		not specified	Uncertain significance (Feb 09, 2022)
6-11538372-C-T		not specified	Uncertain significance (Apr 25, 2023)
6-11565711-T-G		not specified	Uncertain significance (Jun 04, 2024)
6-11575502-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM170B	protein_coding	protein_coding	ENST00000379426	3	45820

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.787	0.208	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	37	65.2	0.567	0.00000317	833
Missense in Polyphen		7	23.121	0.30275		263
Synonymous	0.868	21	26.7	0.786	0.00000149	275
Loss of Function	2.10	0	5.11	0.00	2.19e-7	58

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates the canonical Wnt signaling in breast cancer cells. Exerts an inhibitory effect on breast cancer growth by inhibiting CTNNB1 stabilization and nucleus translocation, which reduces the activity of Wnt targets (PubMed:29367600). {ECO:0000269|PubMed:29367600}.

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.340
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem170b

Gene ontology

• Biological process: Wnt signaling pathway;negative regulation of canonical Wnt signaling pathway
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding