PLXDC2

plexin domain containing 2

Basic information

Region (hg38): 10:19816238-20289856

Links

ENSG00000120594 ∙ NCBI:84898 ∙ OMIM:606827 ∙ HGNC:21013 ∙ Uniprot:Q6UX71 ∙ 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 PLXDC2 gene.

• Inborn genetic diseases (17 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLXDC2 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			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	1

Variants in PLXDC2

This is a list of pathogenic ClinVar variants found in the PLXDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-19817084-C-A		not specified	Uncertain significance (Mar 06, 2023)
10-19817087-G-A		not specified	Uncertain significance (Jun 07, 2023)
10-19817093-C-G		not specified	Uncertain significance (Sep 26, 2023)
10-19817149-C-A		not specified	Uncertain significance (Jan 09, 2024)
10-19817156-A-G		not specified	Likely benign (Jan 16, 2024)
10-20001841-C-T		not specified	Uncertain significance (Dec 16, 2022)
10-20001883-C-T			Benign (Jan 08, 2018)
10-20001906-G-A			Likely benign (May 14, 2018)
10-20046870-A-T		not specified	Uncertain significance (Jan 03, 2022)
10-20046875-A-G		not specified	Uncertain significance (May 25, 2022)
10-20046926-A-C		not specified	Uncertain significance (Oct 03, 2023)
10-20046930-G-A		not specified	Uncertain significance (Sep 14, 2023)
10-20046949-A-G		not specified	Uncertain significance (Feb 05, 2024)
10-20143325-G-A		not specified	Uncertain significance (Jul 12, 2023)
10-20147867-C-A		not specified	Uncertain significance (Jan 17, 2024)
10-20177014-C-A		not specified	Uncertain significance (Dec 21, 2022)
10-20177043-C-A		not specified	Uncertain significance (Mar 14, 2023)
10-20177352-G-A		not specified	Uncertain significance (Apr 05, 2023)
10-20211673-T-C		not specified	Uncertain significance (Dec 19, 2023)
10-20217475-G-A		not specified	Likely benign (Nov 06, 2023)
10-20217496-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-20217531-A-G		not specified	Uncertain significance (Dec 27, 2023)
10-20217562-G-A		not specified	Uncertain significance (Aug 15, 2023)
10-20245365-G-T		not specified	Uncertain significance (Apr 04, 2023)
10-20245416-A-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLXDC2	protein_coding	protein_coding	ENST00000377252	14	473618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.134	0.866	125731	0	13	125744	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.772	260	297	0.874	0.0000153	3448
Missense in Polyphen		66	101.41	0.65082		1178
Synonymous	-0.324	115	111	1.04	0.00000612	1015
Loss of Function	3.92	8	31.8	0.251	0.00000189	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.0000624	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000103	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in tumor angiogenesis. {ECO:0000269|PubMed:11559528}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.508
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• pHI: 0.461
• hipred: N
• hipred_score: 0.492
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.351

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plxdc2

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding