DALRD3

DALR anticodon binding domain containing 3, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 3:49015487-49022293

Links

ENSG00000178149 ∙ NCBI:55152 ∙ OMIM:618904 ∙ HGNC:25536 ∙ Uniprot:Q5D0E6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
• developmental and epileptic encephalopathy, 86 (Limited), mode of inheritance: AR
• developmental and epileptic encephalopathy, 86 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epileptic encephalopathy, early infantile, 86	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	32427860

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DALRD3 gene.

• Inborn genetic diseases (23 variants)
• not provided (8 variants)
• Developmental and epileptic encephalopathy, 86 (2 variants)
• DALRD3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DALRD3 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				4		4
missense			23		1	24
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3		1	4
Total	0	0	27	4	2

Variants in DALRD3

This is a list of pathogenic ClinVar variants found in the DALRD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49015608-G-A		not specified	Uncertain significance (Sep 21, 2023)
3-49015634-T-C		not specified	Uncertain significance (Nov 21, 2022)
3-49015671-G-A		not specified	Uncertain significance (Jun 22, 2021)
3-49015786-A-G			Benign (Feb 20, 2022)
3-49015850-A-C		not specified	Uncertain significance (May 18, 2022)
3-49016004-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-49016067-A-G		not specified	Uncertain significance (May 05, 2023)
3-49016070-A-C		not specified	Uncertain significance (Mar 06, 2023)
3-49016160-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-49016186-C-T		not specified	Uncertain significance (Nov 30, 2022)
3-49016236-G-T		Developmental and epileptic encephalopathy, 86	Conflicting classifications of pathogenicity (Mar 29, 2024)
3-49016261-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-49016262-G-A		Developmental and epileptic encephalopathy, 86	Uncertain significance (Apr 25, 2021)
3-49016306-G-A		not specified	Uncertain significance (Feb 26, 2024)
3-49016485-C-T			Likely benign (Apr 01, 2024)
3-49016641-G-A		not specified	Uncertain significance (Nov 03, 2022)
3-49016658-C-A		not specified	Uncertain significance (Nov 18, 2022)
3-49016843-T-A		not specified	Uncertain significance (Dec 17, 2021)
3-49017259-T-C			Benign (Apr 19, 2019)
3-49017268-A-T		not specified	Uncertain significance (Apr 04, 2023)
3-49017335-T-G		not specified	Uncertain significance (Apr 04, 2023)
3-49017455-G-T			Likely benign (Sep 01, 2023)
3-49017492-A-G		not specified	Uncertain significance (Aug 14, 2023)
3-49017631-T-TGG			Uncertain significance (Nov 01, 2022)
3-49017664-C-T		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DALRD3	protein_coding	protein_coding	ENST00000341949	12	6806

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.69e-10	0.378	125619	0	129	125748	0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.273	269	282	0.954	0.0000142	3414
Missense in Polyphen		71	78.935	0.89948		1002
Synonymous	0.0488	116	117	0.994	0.00000576	1181
Loss of Function	1.03	18	23.4	0.771	0.00000107	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000979	0.000979
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000611	0.000607
Middle Eastern	0.000979	0.000979
South Asian	0.000298	0.000294
Other	0.000509	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0875

Intolerance Scores

• loftool: 0.701
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.776
• hipred: N
• hipred_score: 0.178
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.528

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dalrd3

Gene ontology

• Biological process: arginyl-tRNA aminoacylation
• Molecular function: arginine-tRNA ligase activity;protein binding;ATP binding