TMEM161B

protein-coding

transmembrane protein 161B

Gene summary

Predicted to enable nucleic acid binding activity. Predicted to be involved in regulation of cardiac muscle cell action potential and regulation of heart rate. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_153354.5

Inheritance

ClinVar variants

U:40B:3

Top phenotype

TMEM161B-related lissencephaly

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr5:88,189,633-88,269,476

External References & Databases

Ensembl (ENSG00000164180)

Transcript & Mutation Effects

hg38 • Region Span ~79.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM161B variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 32

not providedTotal: 2

TMEM161B-related lissencephalyTotal: 2

PolymicrogyriaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153354.5. 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			1 clinvar		1 clinvar	2
missense			33 clinvar	2 clinvar		35
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	40	2	1	43

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153354.5	RefSeq	NP_699185.1	12	MANE Select
ENST00000296595.11	Ensembl	ENSP00000296595.6	12	MANE Select
NM_001289007.2	RefSeq	NP_001275936.1	13	Standard
NM_001289008.2	RefSeq	NP_001275937.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296595
Coding exons: 12
Length: 79844
Individuals with no LoFs: 125565
Homozygous LoFs: 0
Heterozygous LoFs: 177
Defined: 125742
p: 0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	191	243	0.785	0.0000114	3153
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00088	0.00086	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.0011	0.0011	notable
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.0010	0.0010	notable
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.329
RVIS EVS: -0.01
RVIS percentile EVS: 53.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.199

Gene Damage Prediction

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