TMEM139

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
missense			32 clinvar	2 clinvar		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	2	0	35

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001282876.2	RefSeq	NP_001269805.1	2	MANE Select
ENST00000359333.8	Ensembl	ENSP00000352284.3	2	MANE Select
NM_001242773.2	RefSeq	NP_001229702.1	2	Standard
NM_001242774.3	RefSeq	NP_001229703.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359333
Coding exons: 2
Length: 8092
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125744
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.214	130	123	1.05	0.00000689	1368
Missense (PolyPhen)		35	31.689	1.1045		356
Synonymous	0.437	47	51.0	0.922	0.00000276	476
Loss of Function	0.981	4	6.75	0.593	3.72e-7	77

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.000099	0.000098	rare
Other	0.00020	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in cellular trafficking of proteins such as SLC4A1. {ECO:0000305|PubMed:26049106}.;

Recessive Scores

pRec: 0.0402

Intolerance Scores

LoFtool: 0.398
RVIS EVS: 0.7
RVIS percentile EVS: 85.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00938

Gene Damage Prediction

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