PXDC1

PX domain containing 1

Basic information

Region (hg38): 6:3722614-3751713

Previous symbols: [ "C6orf145" ]

Links

ENSG00000168994 ∙ NCBI:221749 ∙ ∙ HGNC:21361 ∙ Uniprot:Q5TGL8 ∙ 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 PXDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXDC1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in PXDC1

This is a list of pathogenic ClinVar variants found in the PXDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-3727554-T-C		not specified	Uncertain significance (Sep 06, 2022)
6-3727556-C-A		not specified	Uncertain significance (Sep 20, 2023)
6-3727563-G-A		not specified	Uncertain significance (May 01, 2024)
6-3727566-T-A		not specified	Uncertain significance (Dec 03, 2021)
6-3737105-C-T		not specified	Uncertain significance (Oct 26, 2021)
6-3737108-G-A		not specified	Uncertain significance (Oct 04, 2022)
6-3737186-G-A		not specified	Uncertain significance (May 09, 2022)
6-3738079-G-A		not specified	Uncertain significance (Apr 25, 2022)
6-3738143-C-T		not specified	Uncertain significance (Apr 25, 2022)
6-3751282-G-A		not specified	Uncertain significance (Dec 11, 2023)
6-3751309-G-A		not specified	Uncertain significance (Jun 06, 2023)
6-3751336-G-A		not specified	Uncertain significance (Apr 09, 2024)
6-3751402-C-G		not specified	Uncertain significance (Dec 07, 2021)
6-3751434-C-T		not specified	Uncertain significance (Jul 09, 2024)
6-3751435-C-T		not specified	Uncertain significance (Feb 28, 2024)
6-3751490-C-A		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXDC1	protein_coding	protein_coding	ENST00000380283	5	29413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00433	0.879	125736	0	5	125741	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.722	104	127	0.820	0.00000626	1489
Missense in Polyphen		41	62.932	0.65149		790
Synonymous	-1.64	67	52.0	1.29	0.00000318	429
Loss of Function	1.33	5	9.39	0.532	3.97e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.327
• hipred: N
• hipred_score: 0.377
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pxdc1

Gene ontology

• Molecular function: phosphatidylinositol binding