KCNJ13

Chr 2ARAD

potassium inwardly rectifying channel subfamily J member 13

Also known as: KIR1.4, KIR7.1, LCA16, SVD

NCBI Gene: 3769 ENSG00000115474 UniProt: O60928 OMIM: 603208

This gene encodes an inwardly rectifying potassium channel that allows potassium ions to flow into cells, with characteristically low conductance and minimal sensitivity to typical channel blockers. Mutations cause Leber congenital amaurosis 16 and snowflake vitreoretinal degeneration, both affecting retinal function and vision. The gene shows both autosomal recessive and autosomal dominant inheritance patterns depending on the specific condition.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a member of the inwardly rectifying potassium channel family of proteins. Members of this family form ion channel pores that allow potassium ions to pass into a cell. The encoded protein belongs to a subfamily of low signal channel conductance proteins that have a low dependence on potassium concentration. Mutations in this gene are associated with snowflake vitreoretinal degeneration. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Feb 2010]

GeneReviews OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Leber congenital amaurosis 16MIM #614186

Snowflake vitreoretinal degenerationMIM #193230

Clinical highlights

Gene–disease validity (ClinGen)

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.86

LOEUF

LOF*

Mechanism· G2P

📖

GeneReview available — KCNJ13

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.86LOEUF

pLI 0.014

Z-score 1.92

OE 0.41 (0.21–0.86)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.93Z-score

OE missense 0.62 (0.53–0.71)

123 obs / 199.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.41 (0.21–0.86)

0≤0.351.4

Missense OE?0.62 (0.53–0.71)

0≤0.61.4

Synonymous OE?0.86

0≤1.21.6

LoF obs/exp: 5 / 12.2Missense obs/exp: 123 / 199.9Syn Z: 0.91

Background carrier burden — how many people carry a rare variant somewhere in KCNJ13?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 270

361 rare PASS variants

Rare truncating (LoF)

1 in 3,300

38 rare PASS variants

Rare synonymous (reference)

1 in 920

139 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for KCNJ13. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 360	1 in 4,700
South Asian	~43k	1 in 160	≈ 1 in 11,000
Remaining (unassigned)	~30k	1 in 240	1 in 3,000
European (Finnish)	~27k	1 in 1,500	≈ 1 in 13,000
Admixed American	~22k	1 in 300	none seen
African / African American	~21k	1 in 200	1 in 3,300
East Asian	~20k	1 in 250	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 300	≈ 1 in 4,300
Middle Eastern	~2,884	1 in 150	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓