PXT1

peroxisomal testis enriched protein 1

Basic information

Region (hg38): 6:36390551-36442854

Links

ENSG00000179165 ∙ NCBI:222659 ∙ ∙ HGNC:18312 ∙ Uniprot:Q8NFP0 ∙ 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 PXT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXT1 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in PXT1

This is a list of pathogenic ClinVar variants found in the PXT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-36391831-A-G		not specified	Uncertain significance (May 15, 2024)
6-36391863-C-G		not specified	Uncertain significance (Mar 06, 2023)
6-36391867-T-C		not specified	Uncertain significance (Oct 03, 2024)
6-36400504-T-G		not specified	Uncertain significance (Feb 27, 2024)
6-36400527-T-C		not specified	Uncertain significance (Apr 19, 2024)
6-36400535-A-C		not specified	Uncertain significance (Dec 13, 2024)
6-36400537-G-A		not specified	Uncertain significance (Sep 26, 2022)
6-36400538-C-G		not specified	Likely benign (May 02, 2024)
6-36400581-T-C		not specified	Uncertain significance (Jan 22, 2024)
6-36426042-T-G		not specified	Uncertain significance (Jan 27, 2025)
6-36426066-T-C		not specified	Uncertain significance (Jan 04, 2024)
6-36426070-G-A		not specified	Uncertain significance (Sep 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXT1	protein_coding	protein_coding	ENST00000454782	3	52339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000252	0.0937	125716	0	11	125727	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0856	63	61.1	1.03	0.00000264	902
Missense in Polyphen		12	16.514	0.72666		259
Synonymous	0.820	16	20.8	0.771	8.93e-7	224
Loss of Function	-1.22	7	4.28	1.64	1.80e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000953	0.0000953
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000943	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.611
• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.83

Haploinsufficiency Scores

• pHI: 0.329
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.865

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pxt1

Gene ontology

• Biological process: biological_process;positive regulation of apoptotic process
• Cellular component: nucleus;peroxisome
• Molecular function: molecular_function