PXMP2

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			36 clinvar	3 clinvar		39
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	39	4	1	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018663.3	RefSeq	NP_061133.1	5	MANE Select
ENST00000317479.8	Ensembl	ENSP00000321271.3	5	MANE Select
ENST00000428960.3	Ensembl	ENSP00000398708.3	5	Standard
ENST00000454379.2	Ensembl	ENSP00000484702.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Peroxisome - Homo sapiens (human)
Signaling by GPCR
Signal Transduction
Metabolism of amino acids and derivatives
Metabolism

Biological Process

biological_process

Molecular Function

protein binding

Cellular Component

cytoplasm
peroxisomal membrane
membrane
integral component of membrane
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317479
Coding exons: 5
Length: 33085
Individuals with no LoFs: 124519
Homozygous LoFs: 12
Heterozygous LoFs: 1217
Defined: 125748
p: 0.00490

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.495	113	99.1	1.14	0.00000603	1228
Missense (PolyPhen)		32	29.007	1.1032		348
Synonymous	0.475	40	44.0	0.909	0.00000296	404
Loss of Function	1.10	4	7.17	0.558	3.05e-7	91

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0015	notable
Latino/Admixed American	0.0018	0.0018	notable
Ashkenazi Jewish	0.011	0.010	notable
East Asian	0.00050	0.00049	rare
Finnish	0.0026	0.0025	notable
European (Non-Finnish)	0.0029	0.0029	notable
South Asian	0.020	0.020	notable
Other	0.0059	0.0059	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the peroxisomal membrane.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.327
RVIS EVS: -0.43
RVIS percentile EVS: 25.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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