KCTD7

Chr 7AR

potassium channel tetramerization domain containing 7

Also known as: CLN14, EPM3

This gene encodes a member of the potassium channel tetramerization domain-containing protein family. Family members are identified on a structural basis and contain an amino-terminal domain similar to the T1 domain present in the voltage-gated potassium channel. Mutations in this gene have been associated with progressive myoclonic epilepsy-3. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jan 2011]

GeneReviewsOMIMResearchGenerating clinical summary…
LOFmechanismARLOEUF 0.651 OMIM phenotype
Clinical SummaryKCTD7
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Gene-Disease Validity (ClinGen)
progressive myoclonus epilepsy · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
41 unique Pathogenic / Likely Pathogenic· 215 VUS of 475 total submissions
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
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GeneReview available — KCTD7
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.65LOEUF
pLI 0.001
Z-score 2.90
OE 0.39 (0.240.65)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
1.47Z-score
OE missense 0.75 (0.670.84)
210 obs / 279.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.39 (0.240.65)
00.351.4
Missense OE?0.75 (0.670.84)
00.61.4
Synonymous OE?0.90
01.21.6
LoF obs/exp: 10 / 25.9Missense obs/exp: 210 / 279.0Syn Z: 0.75
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveKCTD7-related progressive myoclonic epilepsyLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6936th %ile
GOF
0.5856th %ile
LOF
0.2776th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

475 submitted variants in ClinVar

Classification Summary

Pathogenic21
Likely Pathogenic20
VUS215
Likely Benign168
Benign25
Conflicting24
21
Pathogenic
20
Likely Pathogenic
215
VUS
168
Likely Benign
25
Benign
24
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
12
4
5
0
21
Likely Pathogenic
8
10
1
1
20
VUS
1
148
63
3
215
Likely Benign
0
0
76
92
168
Benign
0
0
23
2
25
Conflicting
24
Total2116216898473

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

View in ClinVar →

18 pathogenic / likely-pathogenic (of 27) ClinVar copy-number / structural variants overlap KCTD7 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

KCTD7 · protein map & ClinVar variants

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