SLC7A6OS

protein-coding

solute carrier family 7 member 6 opposite strand

Gene summary

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]

MANE transcript

NM_032178.3

Inheritance

ClinVar variants

P:1U:52B:9

Top phenotype

Epilepsy, progressive myoclonic, 12

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr16:68,284,503-68,310,946

External References & Databases

Ensembl (ENSG00000103061)

Transcript & Mutation Effects

hg38 • Region Span ~26.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

epilepsy, progressive myoclonic, 12LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030936

Submitter: Labcorp Genetics (formerly Invitae)

epilepsy, progressive myoclonic, 12LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030936

Submitter: PanelApp Australia

epilepsyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0005027

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Epilepsy, progressive myoclonic, 12AR

Manifestation: Neurologic

Intervention: General

Rationale: 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

Refs: 33085104

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC7A6OS variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 10

Epilepsy, progressive myoclonic, 12Total: 3

Generalized myoclonic seizureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032178.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar		5
missense		1 clinvar	50 clinvar	3 clinvar	1 clinvar	55
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	52	8	1	62

Highest pathogenic variant AF is 0.0000130826775

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032178.3	RefSeq	NP_115554.2	5	MANE Select
ENST00000263997.11	Ensembl	ENSP00000263997.5	5	MANE Select
ENST00000561590.1	Ensembl	ENSP00000461470.1	2	Standard
ENST00000568315.1	Ensembl	ENSP00000462436.1	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
slc7a6os	Danio rerio	Structure: whole organism Quality: immobile abnormal

Gene / Model

Organism

Observed Phenotype

slc7a6os

Danio rerio

Structure: whole organism

Quality: immobile

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

hematopoietic progenitor cell differentiation
protein transport
developmental process

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263997
Coding exons: 5
Length: 26444
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.178	175	182	0.963	0.00000930	1987
Missense (PolyPhen)		49	58.111	0.84321		654
Synonymous	-1.28	91	76.7	1.19	0.00000421	591
Loss of Function	2.62	4	14.9	0.268	7.22e-7	169

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000061	0.000058	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Directs RNA polymerase II nuclear import. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.347
RVIS EVS: 0.75
RVIS percentile EVS: 86.57

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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