PLXDC1

plexin domain containing 1

Basic information

Region (hg38): 17:39063312-39154394

Links

ENSG00000161381 ∙ NCBI:57125 ∙ OMIM:606826 ∙ HGNC:20945 ∙ Uniprot:Q8IUK5 ∙ 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 PLXDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLXDC1 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in PLXDC1

This is a list of pathogenic ClinVar variants found in the PLXDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-39067851-C-T		not specified	Uncertain significance (May 21, 2024)
17-39067898-G-A		not specified	Uncertain significance (May 17, 2023)
17-39067934-A-G		not specified	Uncertain significance (Feb 17, 2024)
17-39067949-T-G		not specified	Uncertain significance (Jul 13, 2022)
17-39069864-A-G		not specified	Uncertain significance (Nov 08, 2022)
17-39069930-C-T		not specified	Uncertain significance (Nov 15, 2021)
17-39069957-C-G		not specified	Uncertain significance (Mar 15, 2024)
17-39072455-C-T		not specified	Uncertain significance (Apr 19, 2023)
17-39079115-A-G		not specified	Uncertain significance (Oct 17, 2023)
17-39079139-G-A		not specified	Uncertain significance (May 03, 2023)
17-39079145-G-A		not specified	Uncertain significance (Sep 06, 2022)
17-39083496-G-C		not specified	Uncertain significance (Jun 18, 2021)
17-39083519-C-T		not specified	Uncertain significance (Jul 08, 2021)
17-39087622-A-G		not specified	Uncertain significance (Apr 07, 2023)
17-39087648-T-C		not specified	Uncertain significance (Dec 17, 2023)
17-39087685-T-C		not specified	Uncertain significance (Jun 22, 2021)
17-39087690-C-T		not specified	Uncertain significance (Feb 13, 2023)
17-39087696-C-T		not specified	Uncertain significance (Jan 26, 2022)
17-39105883-A-G		not specified	Uncertain significance (Sep 20, 2023)
17-39105922-G-A		not specified	Uncertain significance (Oct 02, 2023)
17-39107444-A-G		not specified	Uncertain significance (Feb 14, 2023)
17-39107475-C-T		not specified	Uncertain significance (Mar 02, 2023)
17-39107484-C-G		not specified	Uncertain significance (Jun 24, 2022)
17-39108153-C-T		not specified	Uncertain significance (May 26, 2022)
17-39108928-G-A		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLXDC1	protein_coding	protein_coding	ENST00000315392	14	91092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-7	0.951	125701	0	46	125747	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	252	302	0.834	0.0000177	3276
Missense in Polyphen		78	96.669	0.80688		1039
Synonymous	1.01	106	120	0.882	0.00000766	967
Loss of Function	1.93	15	25.5	0.588	0.00000126	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000736	0.000731
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000275	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000275	0.000272
South Asian	0.000264	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a critical role in endothelial cell capillary morphogenesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.782
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.315
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.463

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plxdc1

Gene ontology

• Biological process: angiogenesis;spinal cord development
• Cellular component: extracellular region;cytoplasm;plasma membrane;bicellular tight junction;integral component of membrane;dendrite;neuronal cell body;receptor complex
• Molecular function: protein binding