GKN2

protein-coding

gastrokine 2, the group of BRICHOS domain containing

Gene summary

The secretory protein encoded by this gene is produced in gastric surface mucous cells, where it can bind trefoil factor family peptide 1 or gastrokine-1. This gene may be a tumor suppressor gene, as its expression is markedly decreased in gastric cancer tissues. The encoded protein interacts with gastrokine-1 and regulates homeostasis of the gastric mucosa. [provided by RefSeq, Dec 2015]

MANE transcript

NM_182536.3

Inheritance

—

ClinVar variants

U:23B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr2:68,945,232-68,952,893

External References & Databases

Ensembl (ENSG00000183607)

Transcript & Mutation Effects

hg38 • Region Span ~7.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GKN2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 24

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182536.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			23 clinvar	1 clinvar		24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	1	0	24

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182536.3	RefSeq	NP_872342.2	6	MANE Select
ENST00000328895.9	Ensembl	ENSP00000329292.4	6	MANE Select
ENST00000481498.1	Ensembl	ENSP00000428538.1	5	Standard
ENST00000481498.2	Ensembl	ENSP00000428538.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to bacterium

Cellular Component

extracellular space
basal part of cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328895
Coding exons: 6
Length: 7739
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125744
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.645	116	98.0	1.18	0.00000452	1208
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.00018	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0846

Intolerance Scores

LoFtool: 0.701
RVIS EVS: 0.55
RVIS percentile EVS: 81.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.000255

Gene Damage Prediction

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