KCNJ13

potassium inwardly rectifying channel subfamily J member 13, the group of Potassium inwardly rectifying channel subfamily J

Basic information

Region (hg38): 2:232765801-232776565

Links

ENSG00000115474 ∙ NCBI:3769 ∙ OMIM:603208 ∙ HGNC:6259 ∙ Uniprot:O60928 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Leber congenital amaurosis (Supportive), mode of inheritance: AD
• snowflake vitreoretinal degeneration (Supportive), mode of inheritance: AD
• Leber congenital amaurosis 16 (Strong), mode of inheritance: AR
• snowflake vitreoretinal degeneration (Strong), mode of inheritance: AD
• Leber congenital amaurosis 16 (Definitive), mode of inheritance: AR
• snowflake vitreoretinal degeneration (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Snowflake vitreoretinal degeneration; Leber congenital amaurosis 16	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	4812083; 15557460; 18179896; 18309337; 21763485

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCNJ13 gene.

• not provided (152 variants)
• Leber congenital amaurosis 16 (52 variants)
• Inborn genetic diseases (11 variants)
• Leber congenital amaurosis (5 variants)
• Snowflake vitreoretinal degeneration (2 variants)
• Retinal dystrophy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNJ13 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	38		39
missense		3	92	1	2	98
nonsense			4			4
start loss						0
frameshift		1	2			3
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1			1
non coding			38	5	5	48
Total	0	4	138	44	7

Highest pathogenic variant AF is 0.00000657

Variants in KCNJ13

This is a list of pathogenic ClinVar variants found in the KCNJ13 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-232765867-G-A		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232765966-C-T		Leber congenital amaurosis 16	Likely benign (Jan 13, 2018)
2-232766038-C-T		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232766184-A-C		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232766310-A-T		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232766324-A-G		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232766352-T-C		Leber congenital amaurosis 16	Benign (Jan 13, 2018)
2-232766387-C-T		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232766433-A-T		Leber congenital amaurosis 16	Uncertain significance (Jan 12, 2018)
2-232766434-T-A		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232766448-G-GA		Leber congenital amaurosis	Uncertain significance (Jun 14, 2016)
2-232766473-A-G		Leber congenital amaurosis 16	Uncertain significance (Jan 12, 2018)
2-232766556-A-G		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232766638-A-C		Leber congenital amaurosis 16	Uncertain significance (Jan 12, 2018)
2-232766691-C-T		Leber congenital amaurosis 16	Uncertain significance (Jan 12, 2018)
2-232766706-CTTT-C		Leber congenital amaurosis	Uncertain significance (Jun 14, 2016)
2-232766990-G-A		Leber congenital amaurosis 16	Conflicting classifications of pathogenicity (Jan 01, 2023)
2-232766996-C-A		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232767032-A-G		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232767103-A-G		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232767234-T-C		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232767335-T-C		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)
2-232767407-A-G		Leber congenital amaurosis 16	Uncertain significance (Jan 12, 2018)
2-232767430-G-A		Leber congenital amaurosis 16	Likely benign (Jan 13, 2018)
2-232767499-A-G		Leber congenital amaurosis 16	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNJ13	protein_coding	protein_coding	ENST00000233826	2	10105

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0137	0.959	125716	0	6	125722	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	123	200	0.615	0.0000104	2380
Missense in Polyphen		29	80.744	0.35916		999
Synonymous	0.914	61	70.8	0.862	0.00000359	727
Loss of Function	1.92	5	12.2	0.409	8.26e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. Their voltage dependence is regulated by the concentration of extracellular potassium; as external potassium is raised, the voltage range of the channel opening shifts to more positive voltages. The inward rectification is mainly due to the blockage of outward current by internal magnesium. KCNJ13 has a very low single channel conductance, low sensitivity to block by external barium and cesium, and no dependence of its inward rectification properties on the internal blocking particle magnesium.
• Disease: DISEASE: Snowflake vitreoretinal degeneration (SVD) [MIM:193230]: Developmental and progressive hereditary eye disorder that affects multiple tissues within the eye. Diagnostic features of SVD include fibrillar degeneration of the vitreous humor, early-onset cataract, minute crystalline deposits in the neurosensory retina, and retinal detachment. {ECO:0000269|PubMed:18179896}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leber congenital amaurosis 16 (LCA16) [MIM:614186]: A severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. {ECO:0000269|PubMed:21763485}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Protein digestion and absorption - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.0920
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.0572
• hipred: Y
• hipred_score: 0.768
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnj13
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; skeleton phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: kcnj13
• Affected structure: xanthophore
• Phenotype tag: abnormal
• Phenotype quality: spatial pattern

Gene ontology

• Biological process: potassium ion transport;regulation of ion transmembrane transport;potassium ion import across plasma membrane
• Cellular component: integral component of membrane
• Molecular function: inward rectifier potassium channel activity