DPYSL2

dihydropyrimidinase like 2, the group of M38 metallopeptidases

Basic information

Region (hg38): 8:26514030-26658178

Links

ENSG00000092964 ∙ NCBI:1808 ∙ OMIM:602463 ∙ HGNC:3014 ∙ Uniprot:Q16555 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DPYSL2 gene.

• not provided (14 variants)
• Inborn genetic diseases (14 variants)
• DPYSL2-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPYSL2 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				5	4	9
missense		1	15	1	1	18
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	1	16	6	6

Variants in DPYSL2

This is a list of pathogenic ClinVar variants found in the DPYSL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-26514595-CG-C		DPYSL2-related disorder	Uncertain significance (Sep 22, 2023)
8-26581971-C-A		Inborn genetic diseases	Likely pathogenic (Dec 18, 2013)
8-26581971-C-T			Benign (Jul 07, 2018)
8-26582018-C-T			Uncertain significance (Nov 06, 2023)
8-26583859-G-A			Likely benign (Mar 29, 2018)
8-26583943-A-G			Likely benign (Mar 01, 2023)
8-26624181-G-A			Benign (Dec 31, 2019)
8-26624211-G-A		not specified	Uncertain significance (Dec 20, 2023)
8-26624290-C-A		not specified	Uncertain significance (Apr 13, 2023)
8-26624290-C-T		not specified	Uncertain significance (Jun 05, 2023)
8-26624306-C-T			Likely benign (Feb 01, 2023)
8-26626656-G-A		DPYSL2-related disorder	Likely benign (Jun 08, 2023)
8-26627245-A-G		not specified	Uncertain significance (Jun 02, 2023)
8-26627280-C-T		not specified	Likely benign (Jan 08, 2024)
8-26627281-G-A		DPYSL2-related disorder	Uncertain significance (Feb 23, 2024)
8-26627930-G-A		not specified	Uncertain significance (Jan 17, 2024)
8-26634786-G-A		not specified	Uncertain significance (May 03, 2023)
8-26634815-C-T			Benign (Dec 31, 2019)
8-26634820-A-G		not specified	Uncertain significance (Sep 29, 2022)
8-26643481-C-T		not specified	Uncertain significance (Dec 21, 2022)
8-26643482-G-C			Likely benign (Oct 12, 2018)
8-26643502-G-A		not specified	Uncertain significance (Apr 26, 2023)
8-26643534-A-G		not specified	Uncertain significance (Jul 14, 2021)
8-26643976-C-G		not specified	Uncertain significance (Oct 10, 2023)
8-26643977-C-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPYSL2	protein_coding	protein_coding	ENST00000311151	14	143904

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00625	125681	0	3	125684	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.88	159	368	0.432	0.0000228	3755
Missense in Polyphen		41	143.85	0.28502		1387
Synonymous	0.390	138	144	0.959	0.00000964	1134
Loss of Function	4.41	3	28.3	0.106	0.00000139	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000895	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in neuronal development and polarity, as well as in axon growth and guidance, neuronal growth cone collapse and cell migration. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. May play a role in endocytosis. {ECO:0000269|PubMed:11477421, ECO:0000269|PubMed:15466863, ECO:0000269|PubMed:20801876}.
• Pathway: Axon guidance - Homo sapiens (human);Regulation of Microtubule Cytoskeleton;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Olfactory bulb development and olfactory learning;Developmental Biology;Recycling pathway of L1;TCR;Semaphorin interactions;L1CAM interactions;Axon guidance;CRMPs in Sema3A signaling (Consensus)

Recessive Scores

• pRec: 0.546

Intolerance Scores

• loftool: 0.0139
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.548
• hipred: Y
• hipred_score: 0.851
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.620

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpysl2
• 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: dpysl2b
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: displaced to

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;endocytosis;cytoskeleton organization;signal transduction;nervous system development;axon guidance;brain development;regulation of axon extension
• Cellular component: cytosol;microtubule;plasma membrane;membrane;extracellular exosome
• Molecular function: dihydropyrimidinase activity;protein binding;microtubule binding;identical protein binding