PODXL2

podocalyxin like 2

Basic information

Region (hg38): 3:127629185-127672802

Links

ENSG00000114631 ∙ NCBI:50512 ∙ OMIM:616627 ∙ HGNC:17936 ∙ Uniprot:Q9NZ53 ∙ 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 PODXL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PODXL2 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				1		1
missense			47	1		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	2	0

Variants in PODXL2

This is a list of pathogenic ClinVar variants found in the PODXL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-127629224-G-A		not specified	Uncertain significance (Apr 28, 2023)
3-127629226-C-T		not specified	Uncertain significance (Dec 13, 2022)
3-127629244-C-T		not specified	Uncertain significance (Apr 20, 2024)
3-127629284-T-G		not specified	Uncertain significance (Mar 14, 2023)
3-127639361-G-A		not specified	Uncertain significance (Aug 20, 2024)
3-127639404-C-G		not specified	Uncertain significance (Sep 29, 2023)
3-127660425-A-G		not specified	Uncertain significance (Mar 07, 2024)
3-127660426-C-G		not specified	Uncertain significance (Dec 22, 2023)
3-127660449-A-G		not specified	Uncertain significance (Jan 30, 2024)
3-127660609-G-A		not specified	Uncertain significance (Apr 17, 2023)
3-127660633-A-G		not specified	Uncertain significance (Jun 11, 2021)
3-127660642-A-G		not specified	Uncertain significance (Dec 10, 2024)
3-127660677-G-A		not specified	Uncertain significance (Mar 20, 2023)
3-127660690-G-A		not specified	Likely benign (Jun 29, 2023)
3-127660704-G-A		not specified	Uncertain significance (Aug 17, 2022)
3-127660717-C-T		not specified	Uncertain significance (Nov 30, 2021)
3-127660776-C-G		not specified	Uncertain significance (Oct 06, 2021)
3-127660783-C-T		not specified	Uncertain significance (Jan 09, 2024)
3-127660809-A-C		not specified	Uncertain significance (Nov 11, 2024)
3-127660821-G-T		not specified	Uncertain significance (Jan 17, 2024)
3-127660822-C-T		not specified	Uncertain significance (Jul 17, 2023)
3-127660842-G-T		not specified	Uncertain significance (Jan 26, 2022)
3-127660866-G-A		not specified	Uncertain significance (Oct 01, 2024)
3-127660867-A-C		not specified	Uncertain significance (Aug 22, 2022)
3-127660896-A-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PODXL2	protein_coding	protein_coding	ENST00000342480	8	43629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000636	125594	0	1	125595	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.907	271	316	0.856	0.0000169	3881
Missense in Polyphen		77	109.33	0.70431		1308
Synonymous	0.239	126	129	0.973	0.00000719	1255
Loss of Function	4.27	0	21.2	0.00	9.13e-7	271

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)	0.00000881	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a ligand for vascular selectins. Mediates rapid rolling of leukocytes over vascular surfaces through high affinity divalent cation-dependent interactions with E-, P- and L- selectins. {ECO:0000269|PubMed:18606703}.
• Pathway: Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules (Consensus)

Recessive Scores

• pRec: 0.0840

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.369
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.904

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Podxl2

Gene ontology

• Biological process: leukocyte tethering or rolling
• Cellular component: Golgi lumen;integral component of plasma membrane
• Molecular function: protein binding;glycosaminoglycan binding