DPY19L2

dpy-19 like 2

Basic information

Region (hg38): 12:63558913-63668939

Links

ENSG00000177990 ∙ NCBI:283417 ∙ OMIM:613893 ∙ HGNC:19414 ∙ Uniprot:Q6NUT2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 9 (Strong), mode of inheritance: AR
• spermatogenic failure 9 (Strong), mode of inheritance: AR
• male infertility due to globozoospermia (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 9	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	Genitourinary	15533374; 21397063; 21397064; 22627659; 22653751

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DPY19L2 gene.

• Spermatogenic failure 9 (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPY19L2 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				1		1
missense			36	2		38
nonsense	1				1	2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	1	2
Total	1	0	36	4	2

Highest pathogenic variant AF is 0.0000263

Variants in DPY19L2

This is a list of pathogenic ClinVar variants found in the DPY19L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-63560538-C-T		Inborn genetic diseases	Likely benign (Sep 24, 2024)
12-63560545-C-A		Inborn genetic diseases	Uncertain significance (Nov 21, 2024)
12-63560574-C-T		Inborn genetic diseases	Uncertain significance (May 09, 2022)
12-63560575-G-A			Likely benign (Jun 01, 2024)
12-63560577-C-G		Inborn genetic diseases	Uncertain significance (Apr 07, 2022)
12-63560604-G-A		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
12-63569230-C-G		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
12-63569286-T-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
12-63569312-T-A		Spermatogenic failure 9	Pathogenic (Oct 24, 2017)
12-63569344-C-T		Inborn genetic diseases	Uncertain significance (Aug 14, 2023)
12-63570797-G-C		Inborn genetic diseases	Uncertain significance (Aug 28, 2024)
12-63580724-C-T		Inborn genetic diseases	Uncertain significance (Dec 07, 2024)
12-63580746-G-A		Spermatogenic failure 9	Uncertain significance (Nov 10, 2021)
12-63580765-T-C		Inborn genetic diseases	Uncertain significance (Jun 21, 2022)
12-63580785-T-C		Inborn genetic diseases	Uncertain significance (Dec 26, 2023)
12-63580794-T-A		Inborn genetic diseases	Uncertain significance (Nov 17, 2023)
12-63582464-A-T		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
12-63582486-G-T		Inborn genetic diseases	Uncertain significance (Jul 08, 2022)
12-63582515-T-C		Spermatogenic failure 9	Uncertain significance (Jul 22, 2021)
12-63594097-T-A			Likely benign (Dec 05, 2017)
12-63595971-T-C		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
12-63597810-G-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2021)
12-63597856-T-A			Uncertain significance (Jul 01, 2023)
12-63597867-G-C		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
12-63597906-C-A			Likely benign (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPY19L2	protein_coding	protein_coding	ENST00000324472	22	110027

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-13	0.892	125400	1	347	125748	0.00138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.712	345	384	0.898	0.0000194	4927
Missense in Polyphen		80	111.19	0.71951		1438
Synonymous	0.317	129	134	0.965	0.00000667	1413
Loss of Function	2.04	27	41.1	0.657	0.00000197	554

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0179	0.0178
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000328	0.000316
Middle Eastern	0.000109	0.000109
South Asian	0.0000413	0.0000327
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable C-mannosyltransferase that mediates C- mannosylation of tryptophan residues on target proteins (By similarity). Required during spermatogenesis for sperm head elongation and acrosome formation. {ECO:0000250, ECO:0000269|PubMed:21397063, ECO:0000269|PubMed:21397064}.

Intolerance Scores

• loftool: 0.869
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.4

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.495
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpy19l2
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: multicellular organism development;spermatid development;protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan
• Cellular component: nucleus;nuclear inner membrane;integral component of membrane
• Molecular function: mannosyltransferase activity