GKN1

gastrokine 1, the group of BRICHOS domain containing

Basic information

Region (hg38): 2:68974573-68980980

Links

ENSG00000169605 ∙ NCBI:56287 ∙ OMIM:606402 ∙ HGNC:23217 ∙ Uniprot:Q9NS71 ∙ 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 GKN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GKN1 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			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	12	2	0

Variants in GKN1

This is a list of pathogenic ClinVar variants found in the GKN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-68974661-G-A		not specified	Uncertain significance (Nov 15, 2024)
2-68977534-G-T		not specified	Uncertain significance (Feb 23, 2023)
2-68977644-A-C		not specified	Uncertain significance (May 24, 2024)
2-68978881-C-T		not specified	Uncertain significance (Oct 20, 2023)
2-68978933-A-T		not specified	Likely benign (Aug 19, 2024)
2-68978949-C-G		not specified	Uncertain significance (Jul 14, 2024)
2-68978958-G-T		not specified	Uncertain significance (Dec 07, 2024)
2-68978960-T-G		not specified	Uncertain significance (Sep 26, 2024)
2-68979957-G-A		not specified	Uncertain significance (Jul 02, 2024)
2-68979957-G-C		not specified	Uncertain significance (Nov 27, 2023)
2-68979982-G-A		not specified	Uncertain significance (Dec 12, 2022)
2-68980025-G-A		not specified	Uncertain significance (Jan 29, 2024)
2-68980056-G-A		not specified	Likely benign (May 21, 2024)
2-68980063-G-A			Benign (May 08, 2018)
2-68980765-C-A		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GKN1	protein_coding	protein_coding	ENST00000377938	6	6402

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000113	0.206	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.799	86	110	0.785	0.00000551	1329
Missense in Polyphen		18	28.065	0.64137		366
Synonymous	-0.0602	41	40.5	1.01	0.00000234	358
Loss of Function	-0.0454	9	8.85	1.02	3.73e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000299	0.000299
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000110	0.000109
South Asian	0.000686	0.000686
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has mitogenic activity and may be involved in maintaining the integrity of the gastric mucosal epithelium. {ECO:0000269|PubMed:12851218}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.675
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.123
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gkn1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: digestion;positive regulation of cell division
• Cellular component: cellular_component;extracellular space
• Molecular function: molecular_function