PODN

protein-coding

podocan, the group of Small leucine rich repeat proteoglycans

Gene summary

The protein encoded by this gene is a member of the small leucine-rich repeat protein family and contains an amino terminal CX3CXCX7C cysteine-rich cluster followed by a leucine-rich repeat domain. Studies suggest that this protein could function to inhibit smooth muscle cell proliferation and migration following arterial injury. [provided by RefSeq, Jul 2016]

MANE transcript

NM_153703.5

Inheritance

—

ClinVar variants

U:108B:6

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr1:53,062,052-53,085,501

External References & Databases

Ensembl (ENSG00000174348)

Transcript & Mutation Effects

hg38 • Region Span ~23.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PODN variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 2

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153703.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			105 clinvar	5 clinvar		110
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	108	6	0	114

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153703.5	RefSeq	NP_714914.3	9	MANE Select
ENST00000312553.10	Ensembl	ENSP00000308315.6	9	MANE Select
NM_001199080.4	RefSeq	NP_001186009.2	9	Standard
NM_001199081.3	RefSeq	NP_001186010.2	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of cell population proliferation
negative regulation of cell migration

Molecular Function

collagen binding
extracellular matrix structural constituent conferring compression resistance

Cellular Component

extracellular space
cytoplasm
collagen-containing extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000312553
Coding exons: 10
Length: 23321
Individuals with no LoFs: 125651
Homozygous LoFs: 1
Heterozygous LoFs: 96
Defined: 125748
p: 0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.782	355	399	0.890	0.0000278	4177
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00079	0.00037	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00093	0.00071	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00033	0.00032	rare
South Asian	0.0019	0.0012	notable
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.173

Gene Damage Prediction

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