TMEM161A

transmembrane protein 161A

Basic information

Region (hg38): 19:19119169-19138513

Links

ENSG00000064545 ∙ NCBI:54929 ∙ OMIM:618966 ∙ HGNC:26020 ∙ Uniprot:Q9NX61 ∙ 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 TMEM161A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM161A 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			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	1	0

Variants in TMEM161A

This is a list of pathogenic ClinVar variants found in the TMEM161A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19120028-G-A		not specified	Uncertain significance (Oct 17, 2023)
19-19120031-G-A		not specified	Uncertain significance (Dec 27, 2023)
19-19120046-G-A		not specified	Uncertain significance (Jul 08, 2022)
19-19120082-T-C		not specified	Uncertain significance (Feb 11, 2022)
19-19120147-A-G		not specified	Uncertain significance (Aug 17, 2022)
19-19120154-G-C		not specified	Uncertain significance (Oct 29, 2021)
19-19121038-A-T		not specified	Uncertain significance (Feb 13, 2024)
19-19121062-A-G		not specified	Uncertain significance (Oct 14, 2023)
19-19121143-G-A		not specified	Uncertain significance (May 23, 2023)
19-19121332-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-19121359-A-G		not specified	Uncertain significance (Feb 10, 2022)
19-19121389-A-T		not specified	Uncertain significance (Mar 29, 2024)
19-19121546-G-A		not specified	Uncertain significance (Oct 13, 2023)
19-19121564-C-T		not specified	Uncertain significance (Nov 07, 2022)
19-19121640-C-A		not specified	Uncertain significance (Jul 26, 2021)
19-19121640-C-T		not specified	Uncertain significance (May 16, 2022)
19-19121643-G-A		not specified	Uncertain significance (Aug 16, 2022)
19-19130174-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-19130181-C-G		not specified	Likely benign (Jan 03, 2024)
19-19130189-G-A		not specified	Uncertain significance (Oct 29, 2021)
19-19130260-C-A		not specified	Uncertain significance (Jan 10, 2023)
19-19130261-C-T		not specified	Uncertain significance (Sep 17, 2021)
19-19130262-C-G		not specified	Uncertain significance (Dec 28, 2022)
19-19130270-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-19130285-G-A		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM161A	protein_coding	protein_coding	ENST00000162044	12	19345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000110	0.987	125700	0	47	125747	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.574	267	295	0.906	0.0000192	2967
Missense in Polyphen		107	122.38	0.87436		1288
Synonymous	1.15	116	133	0.873	0.00000835	1053
Loss of Function	2.27	14	26.6	0.525	0.00000158	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000937	0.000932
Ashkenazi Jewish	0.00	0.00
East Asian	0.000284	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000805	0.0000791
Middle Eastern	0.000284	0.000272
South Asian	0.000320	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in protection against oxidative stress. Overexpression leads to reduced levels of oxidant-induced DNA damage and apoptosis. {ECO:0000269|PubMed:16551573}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.255
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.229
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem161a

Gene ontology

• Biological process: response to retinoic acid;cellular response to oxidative stress;cellular response to UV;positive regulation of DNA repair;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
• Cellular component: integral component of membrane