NKD1

NKD inhibitor of WNT signaling pathway 1, the group of EF-hand domain containing

Basic information

Region (hg38): 16:50548395-50649249

Links

ENSG00000140807 ∙ NCBI:85407 ∙ OMIM:607851 ∙ HGNC:17045 ∙ Uniprot:Q969G9 ∙ 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 NKD1 gene.

• Inborn genetic diseases (27 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKD1 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	26	1	2

Variants in NKD1

This is a list of pathogenic ClinVar variants found in the NKD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-50548732-G-A		not specified	Uncertain significance (Sep 13, 2023)
16-50549448-T-C		not specified	Uncertain significance (Nov 12, 2021)
16-50608297-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-50608306-G-A		not specified	Uncertain significance (Mar 01, 2024)
16-50608321-A-G		not specified	Uncertain significance (Dec 07, 2023)
16-50608322-C-A		not specified	Uncertain significance (May 09, 2023)
16-50621686-C-A		not specified	Uncertain significance (Aug 14, 2023)
16-50625500-G-A		not specified	Uncertain significance (Jun 29, 2022)
16-50625521-C-T		not specified	Uncertain significance (Aug 15, 2023)
16-50630219-G-T		not specified	Uncertain significance (Dec 15, 2023)
16-50630257-C-G		not specified	Uncertain significance (Aug 08, 2022)
16-50630267-C-T		not specified	Uncertain significance (May 16, 2022)
16-50630270-G-T		not specified	Uncertain significance (Jan 16, 2024)
16-50630294-G-C		not specified	Uncertain significance (Sep 29, 2022)
16-50630315-G-A		not specified	Likely benign (May 18, 2023)
16-50630325-A-G		not specified	Uncertain significance (Feb 23, 2023)
16-50630817-C-T			Benign (Jul 23, 2018)
16-50630887-G-T		not specified	Uncertain significance (Jun 09, 2022)
16-50632281-G-A		not specified	Likely benign (Jan 30, 2024)
16-50632330-G-A		not specified	Uncertain significance (Oct 27, 2022)
16-50633225-C-A		not specified	Uncertain significance (Feb 07, 2023)
16-50633230-C-T		not specified	Uncertain significance (Jun 30, 2023)
16-50633254-C-T		not specified	Uncertain significance (Aug 08, 2023)
16-50633267-C-T		not specified	Uncertain significance (May 18, 2023)
16-50633299-C-G		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKD1	protein_coding	protein_coding	ENST00000268459	10	88407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00656	125018	0	3	125021	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.826	245	284	0.862	0.0000181	3025
Missense in Polyphen		78	108.31	0.72018		1169
Synonymous	-0.265	129	125	1.03	0.00000865	944
Loss of Function	4.14	2	23.8	0.0841	0.00000150	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000898	0.00000886
Middle Eastern	0.00	0.00
South Asian	0.0000379	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell autonomous antagonist of the canonical Wnt signaling pathway. May activate a second Wnt signaling pathway that controls planar cell polarity. {ECO:0000269|PubMed:11752446, ECO:0000269|PubMed:15687260, ECO:0000269|PubMed:16567647}.
• Pathway: Hippo signaling pathway - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);WNT-Ncore;Wnt Signaling Pathway and Pluripotency;Wnt Signaling Pathway;wnt signaling pathway;segmentation clock;multi-step regulation of transcription by pitx2;inactivation of gsk3 by akt causes accumulation of b-catenin in alveolar macrophages;Presenilin action in Notch and Wnt signaling (Consensus)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.0705
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.77

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.851
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nkd1
• Phenotype: craniofacial phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; skeleton phenotype; digestive/alimentary phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: nkd1
• Affected structure: organizer inducing center
• Phenotype tag: abnormal
• Phenotype quality: increased width

Gene ontology

• Biological process: eye photoreceptor cell differentiation;somatic muscle development;Wnt signaling pathway;negative regulation of Wnt signaling pathway;positive regulation of protein catabolic process;negative regulation of canonical Wnt signaling pathway;regulation of cell motility involved in somitogenic axis elongation;positive regulation of non-canonical Wnt signaling pathway via JNK cascade;negative regulation of convergent extension involved in axis elongation;positive regulation of Wnt signaling pathway, planar cell polarity pathway
• Cellular component: protein phosphatase type 2A complex;cytoplasm;plasma membrane
• Molecular function: calcium ion binding;protein binding;PDZ domain binding