DPYSL3

dihydropyrimidinase like 3, the group of M38 metallopeptidases

Basic information

Region (hg38): 5:147390807-147510068

Links

ENSG00000113657 ∙ NCBI:1809 ∙ OMIM:601168 ∙ HGNC:3015 ∙ Uniprot:Q14195 ∙ 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 DPYSL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPYSL3 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				3	2	5
missense			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	23	3	3

Variants in DPYSL3

This is a list of pathogenic ClinVar variants found in the DPYSL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-147394060-C-T		not specified	Uncertain significance (Dec 07, 2021)
5-147394111-T-G		not specified	Uncertain significance (Jan 09, 2024)
5-147395625-G-A		not specified	Uncertain significance (Jul 20, 2021)
5-147395693-C-A		not specified	Uncertain significance (Oct 26, 2021)
5-147395703-C-T		not specified	Uncertain significance (Jun 03, 2022)
5-147395716-T-G			Likely benign (Oct 19, 2017)
5-147397701-C-T		not specified	Uncertain significance (Oct 04, 2022)
5-147397768-C-A		not specified	Uncertain significance (Oct 07, 2022)
5-147399154-C-G			Benign (Mar 29, 2018)
5-147399170-T-C		not specified	Uncertain significance (Dec 21, 2023)
5-147400703-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-147400775-T-C		not specified	Uncertain significance (Dec 19, 2023)
5-147400843-G-A			Benign (Jul 23, 2018)
5-147401553-A-C		not specified	Uncertain significance (Jun 02, 2023)
5-147405667-C-T		not specified	Likely benign (May 30, 2024)
5-147405696-A-G		not specified	Uncertain significance (Oct 12, 2021)
5-147405702-A-G		not specified	Uncertain significance (Oct 04, 2022)
5-147408788-G-C			Benign (Jul 23, 2018)
5-147412658-G-T		not specified	Uncertain significance (Dec 14, 2022)
5-147412669-C-A		not specified	Uncertain significance (Aug 02, 2021)
5-147412679-T-C		not specified	Uncertain significance (May 22, 2023)
5-147413650-G-C		not specified	Uncertain significance (May 26, 2023)
5-147415701-G-A			Benign (Jul 26, 2017)
5-147415769-C-G		not specified	Uncertain significance (Jan 19, 2024)
5-147415828-T-C		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPYSL3	protein_coding	protein_coding	ENST00000343218	14	119246

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00113	125587	0	3	125590	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	271	413	0.657	0.0000223	4499
Missense in Polyphen		108	205.42	0.52575		2237
Synonymous	0.734	151	163	0.927	0.00000919	1363
Loss of Function	4.60	2	28.5	0.0701	0.00000121	351

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)	0.0000268	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance, neuronal growth cone collapse and cell migration (By similarity). {ECO:0000250}.
• Pathway: Developmental Biology;Semaphorin interactions;Axon guidance;CRMPs in Sema3A signaling (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.891
• hipred: Y
• hipred_score: 0.765
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpysl3
• Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: dpysl3
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: displaced to

Gene ontology

• Biological process: positive regulation of neuron projection development;negative regulation of neuron projection development;negative regulation of cell migration;neuron development;response to axon injury;actin filament bundle assembly;protein homooligomerization;positive regulation of filopodium assembly;actin crosslink formation;cellular response to cytokine stimulus
• Cellular component: extracellular space;cytosol;lamellipodium;growth cone;filamentous actin;cell body;synapse;exocytic vesicle
• Molecular function: protein binding;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;SH3 domain binding;filamin binding;chondroitin sulfate binding