DPYSL2

dihydropyrimidinase like 2, the group of M38 metallopeptidases

Basic information

Region (hg38): 8:26514031-26658178

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_specified (43 variants)
not_provided (17 variants)
DPYSL2-related_disorder (5 variants)
Inborn_genetic_diseases (1 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. These statistics are base on transcript: NM_001197293.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				9 clinvar	5 clinvar	14
missense		1 clinvar	43 clinvar	4 clinvar	1 clinvar	49
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	1	44	13	6

Loading clinvar variants...

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