DND1

DND microRNA-mediated repression inhibitor 1, the group of RNA binding motif containing

Basic information

Region (hg38): 5:140670794-140673576

Links

ENSG00000256453 ∙ NCBI:373863 ∙ OMIM:609385 ∙ HGNC:23799 ∙ Uniprot:Q8IYX4 ∙ 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 DND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DND1 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in DND1

This is a list of pathogenic ClinVar variants found in the DND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140671381-G-T		not specified	Uncertain significance (Dec 13, 2023)
5-140671404-A-T		not specified	Uncertain significance (Jan 18, 2022)
5-140671445-G-C		not specified	Uncertain significance (Oct 02, 2023)
5-140671449-G-T		not specified	Uncertain significance (Mar 19, 2024)
5-140671463-G-A		not specified	Uncertain significance (Oct 20, 2024)
5-140671513-C-T		not specified	Uncertain significance (May 23, 2023)
5-140671525-C-T		not specified	Uncertain significance (Mar 24, 2023)
5-140671528-T-C		not specified	Uncertain significance (Feb 10, 2022)
5-140671580-G-C		not specified	Uncertain significance (Jul 27, 2024)
5-140671597-T-C		not specified	Uncertain significance (Nov 14, 2023)
5-140671654-C-T		not specified	Likely benign (May 30, 2024)
5-140671663-G-A		not specified	Uncertain significance (Dec 30, 2023)
5-140671687-C-T		not specified	Uncertain significance (Sep 23, 2023)
5-140672466-C-T		not specified	Uncertain significance (Jan 31, 2022)
5-140672519-G-A		not specified	Uncertain significance (Aug 26, 2022)
5-140672522-G-C		not specified	Uncertain significance (Mar 13, 2023)
5-140672528-G-A		not specified	Uncertain significance (Mar 25, 2024)
5-140672579-G-A		not specified	Uncertain significance (Sep 20, 2023)
5-140672583-G-C		not specified	Uncertain significance (Apr 13, 2022)
5-140672589-G-T		not specified	Uncertain significance (May 28, 2023)
5-140672609-G-C		not specified	Uncertain significance (Dec 03, 2024)
5-140672667-G-A		not specified	Uncertain significance (Jul 05, 2023)
5-140672685-G-A		not specified	Uncertain significance (Jan 10, 2023)
5-140672802-G-C		not specified	Uncertain significance (May 14, 2024)
5-140672898-C-T		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DND1	protein_coding	protein_coding	ENST00000542735	4	2793

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.436	0.563	124834	0	1	124835	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	133	227	0.585	0.0000160	2178
Missense in Polyphen		22	71.081	0.3095		713
Synonymous	0.917	93	105	0.886	0.00000776	745
Loss of Function	2.74	3	14.1	0.213	7.97e-7	136

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)	0.00000889	0.00000889
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding factor that positively regulates gene expression by prohibiting miRNA-mediated gene suppression. Relieves miRNA repression in germline cells (By similarity). Prohibits the function of several miRNAs by blocking the accessibility of target mRNAs. Sequence-specific RNA-binding factor that binds specifically to U-rich regions (URRs) in the 3' untranslated region (3'-UTR) of several mRNAs. Does not bind to miRNAs. May play a role during primordial germ cell (PGC) survival (By similarity). However, does not seem to be essential for PGC migration (By similarity). {ECO:0000250, ECO:0000269|PubMed:18155131}.
• Pathway: Vitamin D Receptor Pathway (Consensus)

Recessive Scores

• pRec: 0.146

Haploinsufficiency Scores

• pHI: 0.385
• hipred: Y
• hipred_score: 0.622
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnd1
• Phenotype: endocrine/exocrine gland phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Zebrafish Information Network

• Gene name: dnd1
• Affected structure: primordial germ cell
• Phenotype tag: abnormal
• Phenotype quality: decreased cellular motility

Gene ontology

• Biological process: multicellular organism development;germ cell development;mRNA stabilization;negative regulation of gene silencing by miRNA
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;mRNA binding;AU-rich element binding;miRNA binding