SLC7A6OS

Chr 16AR

solute carrier family 7 member 6 opposite strand

Also known as: EPM12, Iwr1

NCBI Gene: 84138 ENSG00000103061 UniProt: Q96CW6 OMIM: 619192

SLC7A6OS directs RNA polymerase II nuclear import and is predicted to be involved in hematopoietic progenitor cell differentiation. Mutations cause progressive myoclonic epilepsy type 12, inherited in an autosomal recessive pattern. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.614).

OMIM ResearchSummary from RefSeq, OMIM, UniProt

Predicted to be involved in developmental process. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in cytoplasm and nucleus. Implicated in progressive myoclonus epilepsy. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

DNmechanismARLOEUF 0.611 OMIM phenotype

Clinical Summary— SLC7A6OS

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.

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ClinVar Variants

51 VUS of 67 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.61LOEUF

pLI 0.168

Z-score 2.62

OE 0.27 (0.13–0.61)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.18Z-score

OE missense 0.96 (0.85–1.09)

175 obs / 181.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.27 (0.13–0.61)

0≤0.351.4

Missense OE?0.96 (0.85–1.09)

0≤0.61.4

Synonymous OE?1.19

0≤1.21.6

LoF obs/exp: 4 / 14.9Missense obs/exp: 175 / 181.8Syn Z: -1.28

This gene — mechanism propensity

0.6357th %ile

GOF

0.2397th %ile

LOF

0.4135th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

67 submitted variants in ClinVar

ClinVar

Classification Summary

VUS51

Likely Benign7

Benign1

Conflicting1

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	1	50	0	0	51
Likely Benign	0	3	0	4	7
Benign	0	1	0	0	1
Conflicting	—				1
Total	1	54	0	4	60

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

View in ClinVar →

22 pathogenic / likely-pathogenic (of 34) ClinVar copy-number / structural variants overlap SLC7A6OS — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →