SLC12A7

Chr 5

solute carrier family 12 member 7

Also known as: KCC4

NCBI Gene: 10723ENSG00000113504UniProt: Q9Y666

Enables protein kinase binding activity. Predicted to be involved in several processes, including chloride ion homeostasis; monoatomic ion transmembrane transport; and potassium ion homeostasis. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

430
ClinVar variants
134
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SLC12A7
🧬
Gene-Disease Validity (ClinGen)
renal tubular acidosis, distal, 2, with progressive sensorineural hearing loss · UDNo Known Disease Relationship

No known disease relationship

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
134 Pathogenic / Likely Pathogenic· 198 VUS of 430 total submissions
Some data sources returned errors (1)

pubmed: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.89LOEUF
pLI 0.000
Z-score 2.23
OE 0.67 (0.51–0.89)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.32Z-score
OE missense 0.86 (0.81–0.92)
622 obs / 722.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.67 (0.51–0.89)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.86 (0.81–0.92)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.21
0≤1.21.6
LoF obs/exp: 35 / 52.4Missense obs/exp: 622 / 722.0Syn Z: -3.05

ClinVar Variant Classifications

430 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic132
Likely Pathogenic2
VUS198
Likely Benign24
Benign74
132
Pathogenic
2
Likely Pathogenic
198
VUS
24
Likely Benign
74
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
132
0
132
Likely Pathogenic
0
0
2
0
2
VUS
0
172
26
0
198
Likely Benign
0
12
5
7
24
Benign
0
3
60
11
74
Total018722518430

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SLC12A7 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools