NKD1

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

Basic information

Region (hg38): 16:50548396-50649249

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.

not_specified (71 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. These statistics are base on transcript: NM_000033119.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			68 clinvar	2 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	68	3	1

Loading clinvar variants...

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