GKN2

gastrokine 2, the group of BRICHOS domain containing

Basic information

Region (hg38): 2:68945232-68952893

Links

ENSG00000183607 ∙ NCBI:200504 ∙ OMIM:618589 ∙ HGNC:24588 ∙ Uniprot:Q86XP6 ∙ 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 GKN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GKN2 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	16	0	0

Variants in GKN2

This is a list of pathogenic ClinVar variants found in the GKN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-68945400-C-T		not specified	Uncertain significance (May 23, 2024)
2-68945404-G-C		not specified	Uncertain significance (Nov 14, 2023)
2-68946367-A-G		not specified	Uncertain significance (Nov 25, 2024)
2-68946413-G-C		not specified	Uncertain significance (Aug 12, 2021)
2-68946447-A-T		not specified	Uncertain significance (Jul 10, 2024)
2-68947149-G-C		not specified	Uncertain significance (Oct 27, 2023)
2-68947152-T-G		not specified	Uncertain significance (Jun 07, 2024)
2-68950148-G-A		not specified	Uncertain significance (Mar 18, 2024)
2-68950185-C-T		not specified	Uncertain significance (May 26, 2024)
2-68950203-C-T		not specified	Uncertain significance (Nov 11, 2024)
2-68950208-G-T		not specified	Uncertain significance (Jul 09, 2024)
2-68950218-C-G		not specified	Uncertain significance (Aug 11, 2024)
2-68950227-T-C		not specified	Uncertain significance (Oct 22, 2021)
2-68950229-C-T		not specified	Likely benign (Jan 08, 2025)
2-68950247-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-68950704-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-68950731-T-C		not specified	Uncertain significance (Sep 11, 2024)
2-68950747-A-T		not specified	Uncertain significance (Jan 01, 2025)
2-68952842-A-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GKN2	protein_coding	protein_coding	ENST00000328895	6	7739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000232	0.769	125721	0	23	125744	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.645	116	98.0	1.18	0.00000452	1208
Missense in Polyphen		26	22.336	1.1641		272
Synonymous	0.306	35	37.4	0.936	0.00000196	343
Loss of Function	1.06	7	10.7	0.651	6.09e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.000176	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0846

Intolerance Scores

• loftool: 0.701
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.0886
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000255

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gkn2
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: response to bacterium
• Cellular component: extracellular space;basal part of cell