TMEM161B

transmembrane protein 161B

Basic information

Region (hg38): 5:88189632-88269476

Links

ENSG00000164180 ∙ NCBI:153396 ∙ ∙ HGNC:28483 ∙ Uniprot:Q8NDZ6 ∙ 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 TMEM161B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM161B 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					2	2
Total	0	0	10	1	2

Variants in TMEM161B

This is a list of pathogenic ClinVar variants found in the TMEM161B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-88196381-T-C		not specified	Uncertain significance (Oct 14, 2023)
5-88196456-T-C		not specified	Likely benign (Dec 14, 2023)
5-88198995-G-A		not specified	Uncertain significance (Jun 16, 2024)
5-88199034-C-T		not specified	Uncertain significance (Apr 06, 2023)
5-88199085-A-G		TMEM161B-related lissencephaly	Uncertain significance (Jul 20, 2022)
5-88199113-A-C		not specified	Uncertain significance (Sep 16, 2021)
5-88202986-G-C		not specified	Uncertain significance (Jan 16, 2024)
5-88205809-C-T		TMEM161B-related lissencephaly	Uncertain significance (Jul 20, 2022)
5-88205838-T-C		not specified	Uncertain significance (Apr 15, 2024)
5-88205899-T-G		not specified	Uncertain significance (Jun 10, 2022)
5-88206451-C-A		not specified	Uncertain significance (Sep 01, 2021)
5-88206464-G-A		not specified	Uncertain significance (Dec 01, 2022)
5-88206498-C-A			Benign (Dec 31, 2019)
5-88206508-G-A			Benign (Dec 31, 2019)
5-88206508-G-GA			Benign (Jan 17, 2024)
5-88207164-A-C		not specified	Uncertain significance (Dec 28, 2022)
5-88225826-G-A		not specified	Uncertain significance (Jan 26, 2022)
5-88228490-C-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM161B	protein_coding	protein_coding	ENST00000296595	12	79844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000124	0.998	125565	0	177	125742	0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	191	243	0.785	0.0000114	3153
Missense in Polyphen		54	94.1	0.57386		1232
Synonymous	0.138	84	85.6	0.981	0.00000406	937
Loss of Function	2.71	13	28.7	0.453	0.00000168	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00104
Ashkenazi Jewish	0.00111	0.00109
East Asian	0.00110	0.00109
Finnish	0.000189	0.000185
European (Non-Finnish)	0.00105	0.00103
Middle Eastern	0.00110	0.00109
South Asian	0.0000983	0.0000980
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.329
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.329
• hipred: N
• hipred_score: 0.492
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem161b
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Cellular component: integral component of membrane