PODN

podocan, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 1:53062052-53085501

Links

ENSG00000174348 ∙ NCBI:127435 ∙ OMIM:608661 ∙ HGNC:23174 ∙ Uniprot:Q7Z5L7 ∙ 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 PODN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PODN 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			42	2		44
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	0	0	44	3	0

Variants in PODN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-53062248-A-G		not specified	Uncertain significance (Oct 06, 2022)
1-53062290-C-T		not specified	Uncertain significance (Apr 26, 2024)
1-53062306-C-G		not specified	Uncertain significance (Dec 13, 2023)
1-53069818-G-A		not specified	Uncertain significance (Feb 10, 2023)
1-53069856-A-G		not specified	Uncertain significance (Feb 13, 2024)
1-53069868-C-T		not specified	Likely benign (Dec 21, 2023)
1-53069869-G-T		not specified	Uncertain significance (Jan 04, 2024)
1-53069919-G-A		not specified	Uncertain significance (May 28, 2024)
1-53070004-C-T		not specified	Uncertain significance (May 24, 2023)
1-53070007-T-G		not specified	Uncertain significance (Jul 28, 2021)
1-53070064-G-A		not specified	Uncertain significance (Mar 22, 2022)
1-53070090-G-A		not specified	Uncertain significance (Mar 25, 2022)
1-53070094-T-C		not specified	Uncertain significance (Mar 06, 2023)
1-53070127-C-T		not specified	Uncertain significance (Jun 09, 2022)
1-53071550-A-G		not specified	Uncertain significance (Feb 27, 2023)
1-53071567-G-C		not specified	Uncertain significance (Nov 30, 2022)
1-53071590-A-T		not specified	Uncertain significance (Jun 12, 2023)
1-53074629-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-53075875-C-A		not specified	Uncertain significance (Sep 21, 2023)
1-53077251-G-A		not specified	Uncertain significance (Mar 28, 2024)
1-53077272-C-T		not specified	Uncertain significance (Aug 04, 2021)
1-53077326-C-A		not specified	Uncertain significance (Dec 06, 2021)
1-53077710-C-T		not specified	Uncertain significance (Mar 08, 2024)
1-53077739-C-T		not specified	Uncertain significance (Dec 30, 2023)
1-53078414-C-T		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PODN	protein_coding	protein_coding	ENST00000312553	10	23321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.57e-10	0.738	125651	1	96	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.782	355	399	0.890	0.0000278	4177
Missense in Polyphen		138	168.49	0.81903		1874
Synonymous	-0.619	201	190	1.06	0.0000129	1459
Loss of Function	1.49	18	26.2	0.687	0.00000168	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000847	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.000925	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000327	0.000316
Middle Eastern	0.000925	0.000707
South Asian	0.00193	0.00118
Other	0.000658	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates cell proliferation and cell migration. {ECO:0000269|PubMed:15063725}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.770
• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.81

Haploinsufficiency Scores

• pHI: 0.218
• hipred: N
• hipred_score: 0.425
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Podn
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of cell population proliferation;negative regulation of cell migration
• Cellular component: extracellular space;cytoplasm;collagen-containing extracellular matrix
• Molecular function: collagen binding;extracellular matrix structural constituent conferring compression resistance