DKKL1

dickkopf like acrosomal protein 1

Basic information

Region (hg38): 19:49361783-49375116

Links

ENSG00000104901 ∙ NCBI:27120 ∙ OMIM:605418 ∙ HGNC:16528 ∙ Uniprot:Q9UK85 ∙ 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 DKKL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DKKL1 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			17	1	3	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	17	1	3

Variants in DKKL1

This is a list of pathogenic ClinVar variants found in the DKKL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49364636-C-T		not specified	Uncertain significance (Jun 30, 2023)
19-49364731-G-C		not specified	Uncertain significance (Mar 25, 2024)
19-49364741-G-T		not specified	Uncertain significance (Nov 09, 2023)
19-49365522-G-T		not specified	Uncertain significance (Nov 24, 2024)
19-49365532-C-G		not specified	Uncertain significance (Sep 27, 2021)
19-49365542-T-G		not specified	Uncertain significance (Mar 29, 2023)
19-49365619-C-A		not specified	Uncertain significance (Apr 17, 2023)
19-49365624-T-A		not specified	Uncertain significance (Feb 28, 2024)
19-49365794-T-G			Benign (Apr 27, 2020)
19-49365812-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-49365842-C-A		not specified	Uncertain significance (Jun 17, 2022)
19-49365856-G-C		not specified	Uncertain significance (Aug 10, 2024)
19-49365857-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-49365869-T-C		not specified	Uncertain significance (Mar 06, 2023)
19-49374732-G-A		not specified	Uncertain significance (Jul 16, 2024)
19-49374737-G-T		not specified	Uncertain significance (Jan 10, 2022)
19-49374750-C-T		not specified	Uncertain significance (Mar 21, 2024)
19-49374796-G-A			Benign (Mar 30, 2018)
19-49374805-T-C		not specified	Uncertain significance (Jul 19, 2023)
19-49374828-C-T		not specified	Uncertain significance (May 31, 2023)
19-49374829-G-A		not specified	Uncertain significance (Sep 08, 2024)
19-49374886-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-49374913-G-A		not specified	Uncertain significance (Oct 24, 2023)
19-49374915-A-G		not specified	Likely benign (May 18, 2023)
19-49374928-A-G		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DKKL1	protein_coding	protein_coding	ENST00000221498	5	13334

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000398	0.650	125712	0	27	125739	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.156	149	144	1.04	0.00000863	1549
Missense in Polyphen		54	47.444	1.1382		533
Synonymous	0.321	58	61.2	0.948	0.00000341	513
Loss of Function	0.719	6	8.22	0.730	4.36e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000358	0.000357
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in fertilization by facilitating sperm penetration of the zona pellucida. May promotes spermatocyte apoptosis, thereby limiting sperm production. In adults, may reduces testosterone synthesis in Leydig cells. Is not essential either for development or fertility. {ECO:0000250|UniProtKB:Q9QZL9}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.736
• rvis_EVS: 1.64
• rvis_percentile_EVS: 96.11

Haploinsufficiency Scores

• pHI: 0.373
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.562

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dkkl1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: penetration of zona pellucida;anatomical structure morphogenesis;positive regulation of apoptotic process;positive regulation of fat cell differentiation;negative regulation of canonical Wnt signaling pathway;extracellular negative regulation of signal transduction;negative regulation of testosterone biosynthetic process
• Cellular component: acrosomal vesicle;extracellular space
• Molecular function: co-receptor binding;receptor antagonist activity