DLK2

delta like non-canonical Notch ligand 2

Basic information

Region (hg38): 6:43450351-43456632

Previous symbols: [ "EGFL9" ]

Links

ENSG00000171462 ∙ NCBI:65989 ∙ ∙ HGNC:21113 ∙ Uniprot:Q6UY11 ∙ 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 DLK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLK2 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				2		2
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	4	0

Variants in DLK2

This is a list of pathogenic ClinVar variants found in the DLK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43450600-G-T		not specified	Uncertain significance (Apr 09, 2024)
6-43450646-A-G		not specified	Uncertain significance (Jun 12, 2023)
6-43450652-G-C		not specified	Uncertain significance (Aug 09, 2021)
6-43450655-C-A			Uncertain significance (Sep 01, 2023)
6-43450804-C-T		not specified	Uncertain significance (Nov 27, 2023)
6-43450837-C-A		not specified	Uncertain significance (Jun 11, 2021)
6-43450840-G-T		not specified	Uncertain significance (Feb 26, 2024)
6-43450863-C-T			Likely benign (Mar 01, 2024)
6-43450909-T-A			Likely benign (Apr 01, 2023)
6-43450963-C-G		not specified	Uncertain significance (Jan 19, 2022)
6-43450973-T-G		not specified	Uncertain significance (Jun 04, 2024)
6-43451096-G-C		not specified	Uncertain significance (Sep 17, 2021)
6-43451108-G-T		not specified	Uncertain significance (Nov 29, 2021)
6-43451122-A-C		not specified	Uncertain significance (Nov 22, 2023)
6-43451182-C-T		not specified	Likely benign (Dec 18, 2023)
6-43451191-A-G		not specified	Uncertain significance (Feb 22, 2023)
6-43451215-G-A		not specified	Uncertain significance (Nov 18, 2022)
6-43451967-C-T		not specified	Uncertain significance (Jul 19, 2022)
6-43452006-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-43452022-C-T		not specified	Uncertain significance (Oct 25, 2023)
6-43452066-G-A		not specified	Uncertain significance (Apr 09, 2024)
6-43453119-C-T		not specified	Uncertain significance (Apr 23, 2024)
6-43453127-G-A		not specified	Uncertain significance (Oct 06, 2021)
6-43454458-G-A			Likely benign (Apr 01, 2023)
6-43454771-C-T		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DLK2	protein_coding	protein_coding	ENST00000357338	5	6281

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.779	0.221	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	164	250	0.657	0.0000153	2458
Missense in Polyphen		47	94.609	0.49678		963
Synonymous	1.12	82	96.0	0.854	0.00000563	804
Loss of Function	2.94	2	13.7	0.146	5.87e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates adipogenesis. {ECO:0000250}.
• Pathway: Canonical and Non-canonical Notch signaling (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.0608
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.244
• hipred: Y
• hipred_score: 0.768
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.751

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dlk2

Zebrafish Information Network

• Gene name: dlk2
• Affected structure: subintestinal vein
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: regulation of fat cell differentiation;negative regulation of Notch signaling pathway
• Cellular component: integral component of membrane
• Molecular function: calcium ion binding;protein homodimerization activity