DDN

dendrin

Basic information

Region (hg38): 12:48995149-48999375

Links

ENSG00000181418 ∙ NCBI:23109 ∙ OMIM:610588 ∙ HGNC:24458 ∙ Uniprot:O94850 ∙ 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 DDN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDN 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			41	1	2	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	2

Variants in DDN

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

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

Position	Type	Phenotype	Significance	ClinVar
12-48996812-G-T		not specified	Uncertain significance (Sep 12, 2023)
12-48996889-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-48996894-T-C			Benign (Mar 26, 2020)
12-48996908-C-G		not specified	Uncertain significance (Dec 01, 2022)
12-48996921-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-48996980-C-A		not specified	Uncertain significance (Nov 14, 2023)
12-48997083-C-G		not specified	Uncertain significance (May 03, 2023)
12-48997084-G-A		not specified	Uncertain significance (Dec 27, 2023)
12-48997123-C-T		not specified	Uncertain significance (Jan 08, 2024)
12-48997129-T-C		not specified	Uncertain significance (Dec 07, 2024)
12-48997161-G-A		not specified	Uncertain significance (Dec 20, 2023)
12-48997188-G-A		not specified	Uncertain significance (May 18, 2023)
12-48997200-C-T		not specified	Likely benign (Jul 06, 2021)
12-48997218-G-C		not specified	Uncertain significance (Sep 27, 2021)
12-48997218-G-T		not specified	Uncertain significance (Sep 27, 2024)
12-48997267-C-A		not specified	Uncertain significance (Jan 06, 2023)
12-48997269-G-A		not specified	Uncertain significance (Sep 13, 2023)
12-48997273-T-C		not specified	Uncertain significance (Aug 12, 2021)
12-48997365-G-A		not specified	Uncertain significance (Feb 05, 2024)
12-48997414-C-T		not specified	Uncertain significance (Jun 18, 2021)
12-48997425-C-G		not specified	Uncertain significance (Mar 20, 2024)
12-48997426-G-C		not specified	Uncertain significance (Dec 19, 2022)
12-48997485-G-T		not specified	Uncertain significance (Jan 26, 2022)
12-48997500-C-A		not specified	Uncertain significance (May 08, 2024)
12-48997618-C-T		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDN	protein_coding	protein_coding	ENST00000421952	2	4161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.359	0.641	125724	0	6	125730	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.534	371	401	0.925	0.0000185	4405
Missense in Polyphen		101	150.99	0.66891		1640
Synonymous	0.0232	176	176	0.998	0.00000834	1628
Loss of Function	3.36	5	22.0	0.227	9.95e-7	210

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	0.0000484	0.0000462
European (Non-Finnish)	0.0000366	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes apoptosis of kidney glomerular podocytes. Podocytes are highly specialized cells essential to the ultrafiltration of blood, resulting in the extraction of urine and the retention of protein (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.317
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.521
• hipred: Y
• hipred_score: 0.584
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0926

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddn

Gene ontology

• Biological process: positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum membrane;dendritic spine membrane;cell projection;perikaryon
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;protein binding