TMEM161A

protein-coding

transmembrane protein 161A

Gene summary

Involved in several processes, including cellular response to UV; regulation of cellular response to stress; and response to retinoic acid. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017814.3

Inheritance

—

ClinVar variants

U:85B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr19:19,119,169-19,138,513

External References & Databases

Ensembl (ENSG00000064545)

Transcript & Mutation Effects

hg38 • Region Span ~19.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM161A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 79

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017814.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			79 clinvar	2 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	85	2	0	87

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017814.3	RefSeq	NP_060284.1	12	MANE Select
ENST00000162044.14	Ensembl	ENSP00000162044.7	12	MANE Select
NM_001256766.3	RefSeq	NP_001243695.1	10	Standard
NM_001411131.1	RefSeq	NP_001398060.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000162044
Coding exons: 12
Length: 19345
Individuals with no LoFs: 125700
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125747
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.574	267	295	0.906	0.0000192	2967
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00044	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.00032	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.959

Gene Damage Prediction

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