NKD2

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

Basic information

Region (hg38): 5:1008801-1038943

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.

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.

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			44	7	3	54
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	9	3

Variants in NKD2

This is a list of pathogenic ClinVar variants found in the NKD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-1009502-C-T		not specified	Uncertain significance (Feb 21, 2024)
5-1009510-A-T		not specified	Uncertain significance (Sep 13, 2023)
5-1009547-C-T		not specified	Uncertain significance (Oct 29, 2021)
5-1009550-G-A		not specified	Uncertain significance (Nov 10, 2022)
5-1009553-A-C		not specified	Uncertain significance (May 13, 2024)
5-1009555-A-G		not specified	Uncertain significance (Dec 22, 2023)
5-1032167-G-A		not specified	Likely benign (Mar 23, 2023)
5-1032188-C-T		not specified	Uncertain significance (Dec 15, 2023)
5-1032189-G-A		not specified	Uncertain significance (May 15, 2024)
5-1033404-G-A		not specified	Uncertain significance (Apr 22, 2022)
5-1033465-C-T		not specified	Uncertain significance (Apr 30, 2024)
5-1033474-C-T		not specified	Likely benign (Oct 04, 2022)
5-1033479-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-1033491-A-G		not specified	Uncertain significance (Apr 25, 2022)
5-1034254-C-T		not specified	Uncertain significance (Jan 10, 2022)
5-1034271-C-T		not specified	Uncertain significance (Oct 14, 2023)
5-1034760-T-A			Benign (Dec 01, 2023)
5-1034772-T-C		not specified	Uncertain significance (Dec 14, 2021)
5-1034808-A-G		not specified	Uncertain significance (Feb 16, 2023)
5-1034856-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-1035391-C-T		not specified	Uncertain significance (Jan 18, 2023)
5-1035392-G-A		not specified	Uncertain significance (May 12, 2024)
5-1035404-G-A			Benign/Likely benign (Dec 01, 2022)
5-1036280-C-T		not specified	Uncertain significance (May 25, 2023)
5-1036294-G-A		not specified	Uncertain significance (Mar 25, 2024)

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