PODNL1

podocan like 1

Basic information

Region (hg38): 19:13931187-13953392

Links

ENSG00000132000 ∙ NCBI:79883 ∙ ∙ HGNC:26275 ∙ Uniprot:Q6PEZ8 ∙ 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 PODNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PODNL1 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			43	4		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	4	0

Variants in PODNL1

This is a list of pathogenic ClinVar variants found in the PODNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-13932834-G-C		not specified	Uncertain significance (Sep 01, 2021)
19-13932842-C-T		not specified	Uncertain significance (Jul 15, 2021)
19-13932854-G-A		not specified	Uncertain significance (Mar 30, 2024)
19-13932862-G-A		not specified	Uncertain significance (Nov 08, 2021)
19-13932920-G-A		not specified	Uncertain significance (Mar 13, 2023)
19-13932931-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-13932946-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-13932970-A-G		not specified	Uncertain significance (Aug 10, 2021)
19-13932979-C-T		not specified	Uncertain significance (Dec 26, 2023)
19-13933019-C-T		not specified	Likely benign (Mar 29, 2023)
19-13933028-G-A		not specified	Uncertain significance (Jun 05, 2023)
19-13933045-T-C		not specified	Uncertain significance (Aug 30, 2021)
19-13933058-T-C		not specified	Uncertain significance (Jun 02, 2023)
19-13933075-G-T		not specified	Uncertain significance (Mar 28, 2023)
19-13933090-G-A		not specified	Likely benign (Jan 31, 2024)
19-13933106-C-T		not specified	Uncertain significance (Dec 07, 2023)
19-13933129-G-A		not specified	Uncertain significance (Jun 27, 2023)
19-13933169-G-A		not specified	Uncertain significance (Nov 30, 2021)
19-13933171-C-T		not specified	Uncertain significance (Feb 02, 2022)
19-13933192-C-G		not specified	Uncertain significance (Nov 27, 2023)
19-13933193-G-A		not specified	Uncertain significance (May 03, 2023)
19-13933253-C-T		not specified	Uncertain significance (Dec 14, 2023)
19-13933256-C-A		not specified	Uncertain significance (Aug 18, 2021)
19-13933336-T-G		not specified	Uncertain significance (Oct 26, 2022)
19-13933345-C-T		not specified	Uncertain significance (Apr 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PODNL1	protein_coding	protein_coding	ENST00000339560	8	22205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.40e-13	0.0137	125639	0	51	125690	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.252	299	312	0.960	0.0000213	3153
Missense in Polyphen		88	101.08	0.87057		1154
Synonymous	0.424	140	147	0.955	0.00000909	1189
Loss of Function	-0.386	18	16.3	1.10	9.63e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000858	0.000764
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.000227	0.000185
European (Non-Finnish)	0.000128	0.000114
Middle Eastern	0.000111	0.000109
South Asian	0.000557	0.000523
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.170
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Podnl1

Gene ontology

• Cellular component: collagen-containing extracellular matrix