DPYSL4

dihydropyrimidinase like 4, the group of M38 metallopeptidases

Basic information

Region (hg38): 10:132186948-132205759

Links

ENSG00000151640 ∙ NCBI:10570 ∙ OMIM:608407 ∙ HGNC:3016 ∙ Uniprot:O14531 ∙ 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 DPYSL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPYSL4 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	0

Variants in DPYSL4

This is a list of pathogenic ClinVar variants found in the DPYSL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-132187095-G-A		not specified	Uncertain significance (Feb 15, 2023)
10-132187101-C-T		not specified	Uncertain significance (Dec 26, 2023)
10-132190753-C-T		not specified	Uncertain significance (Feb 21, 2024)
10-132192662-A-G		not specified	Uncertain significance (May 03, 2023)
10-132192680-G-A		not specified	Uncertain significance (Jun 22, 2021)
10-132192770-C-A		not specified	Uncertain significance (Aug 04, 2023)
10-132192790-C-A		not specified	Uncertain significance (Mar 06, 2023)
10-132192791-G-A		not specified	Uncertain significance (Dec 20, 2022)
10-132192837-T-C		not specified	Uncertain significance (Apr 07, 2022)
10-132194862-G-A		not specified	Uncertain significance (Dec 21, 2022)
10-132194901-C-T		not specified	Uncertain significance (Oct 24, 2024)
10-132194911-C-G		not specified	Uncertain significance (Aug 20, 2024)
10-132194915-C-G		not specified	Uncertain significance (Aug 21, 2023)
10-132194917-G-C		not specified	Uncertain significance (Aug 05, 2024)
10-132196884-A-G		not specified	Uncertain significance (Sep 01, 2021)
10-132196899-C-T		not specified	Uncertain significance (Sep 28, 2021)
10-132196921-A-G		not specified	Uncertain significance (Mar 16, 2024)
10-132197033-T-C		not specified	Uncertain significance (Nov 10, 2024)
10-132197085-G-C		not specified	Uncertain significance (Mar 31, 2024)
10-132198416-A-G		not specified	Uncertain significance (Oct 17, 2024)
10-132198418-C-G		not specified	Uncertain significance (Nov 20, 2024)
10-132198439-G-A		not specified	Uncertain significance (Dec 28, 2022)
10-132198851-G-A		not specified	Uncertain significance (Dec 20, 2023)
10-132198927-T-C		not specified	Uncertain significance (Jul 06, 2024)
10-132198965-C-T		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPYSL4	protein_coding	protein_coding	ENST00000338492	14	18877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-8	0.958	125649	0	65	125714	0.000259

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	330	394	0.837	0.0000266	3728
Missense in Polyphen		106	153.52	0.69047		1484
Synonymous	-0.706	187	175	1.07	0.0000142	1153
Loss of Function	2.02	17	28.7	0.593	0.00000156	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000581	0.000577
Ashkenazi Jewish	0.000130	0.0000993
East Asian	0.000598	0.000598
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000598	0.000598
South Asian	0.000304	0.000294
Other	0.000163	0.000163

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: 0.126

Intolerance Scores

• loftool: 0.183
• rvis_EVS: -1.5
• rvis_percentile_EVS: 3.57

Haploinsufficiency Scores

• pHI: 0.234
• hipred: Y
• hipred_score: 0.604
• ghis: 0.659

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.900

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpysl4
• 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)

Gene ontology

• Biological process: nervous system development;neuron death;neuron projection guidance
• Cellular component: cytosol
• Molecular function: protein binding;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;filamin binding