NKD2

NKD inhibitor of WNT signaling pathway 2, the group of EF-hand domain containing

Basic information

Region (hg38): 5:1008802-1038943

Links

ENSG00000145506

∙ NCBI:85409 ∙ OMIM:607852 ∙ HGNC:17046 ∙ Uniprot:Q969F2 ∙ 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 NKD2 gene.

not_specified (100 variants)
not_provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033120.4. 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				3 clinvar		3
missense			92 clinvar	8 clinvar	3 clinvar	103
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	92	11	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKD2	protein_coding	protein_coding	ENST00000296849	10	30115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-12	0.0282	125262	0	46	125308	0.000184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0981	277	272	1.02	0.0000186	2872
Missense in Polyphen		94	89.211	1.0537		941
Synonymous	0.386	118	123	0.956	0.00000927	896
Loss of Function	-0.0686	18	17.7	1.02	8.32e-7	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000335	0.000327
Finnish	0.000200	0.000185
European (Non-Finnish)	0.000166	0.000159
Middle Eastern	0.000335	0.000327
South Asian	0.000377	0.000359
Other	0.000537	0.000491

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 (By similarity). Required for processing of TGFA and for targeting of TGFA to the basolateral membrane of polarized epithelial cells. {ECO:0000250, ECO:0000269|PubMed:15064403, ECO:0000269|PubMed:17553928}.;
Pathway: Wnt signaling pathway - Homo sapiens (human);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;Canonical Wnt signaling pathway (Consensus)

Recessive Scores

pRec: 0.102

Haploinsufficiency Scores

pHI: 0.139
hipred: Y
hipred_score: 0.549
ghis: 0.402

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nkd2
Phenotype: craniofacial phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype;

Zebrafish Information Network

Gene name: nkd2a
Affected structure: organizer inducing center
Phenotype tag: abnormal
Phenotype quality: increased width

Gene ontology

Biological process: exocytosis;positive regulation of protein processing;Wnt signaling pathway;negative regulation of Wnt signaling pathway;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;Golgi vesicle fusion to target membrane;protein localization to plasma membrane;negative regulation of canonical Wnt signaling pathway;positive regulation of protein localization to plasma membrane
Cellular component: cytoplasm;plasma membrane;basolateral plasma membrane;lateral plasma membrane;cytoplasmic vesicle;exocytic vesicle;cell periphery
Molecular function: calcium ion binding;protein binding;growth factor binding;ubiquitin protein ligase binding;myosin heavy chain binding;ATPase binding