SLC7A6OS

solute carrier family 7 member 6 opposite strand

Basic information

Region (hg38): 16:68284502-68310946

Links

ENSG00000103061 ∙ NCBI:84138 ∙ OMIM:619192 ∙ HGNC:25807 ∙ Uniprot:Q96CW6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epilepsy (Limited), mode of inheritance: AR
• epilepsy, progressive myoclonic, 12 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, progressive myoclonic, 12	AR	General	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	Neurologic	33085104

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC7A6OS gene.

• Inborn genetic diseases (16 variants)
• not provided (8 variants)
• Epilepsy, progressive myoclonic, 12 (2 variants)
• not specified (1 variants)
• Generalized myoclonic seizure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A6OS gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			17	3	1	21
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	6	1

Variants in SLC7A6OS

This is a list of pathogenic ClinVar variants found in the SLC7A6OS region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-68287803-C-T		not specified	Uncertain significance (Dec 04, 2021)
16-68287814-G-A		not specified	Uncertain significance (Jun 22, 2021)
16-68287833-T-C		not specified	Uncertain significance (Oct 22, 2021)
16-68290419-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-68290429-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-68291300-T-A			Benign (Apr 16, 2018)
16-68291575-G-A		SLC7A6-related disorder	Likely benign (Jun 18, 2019)
16-68291598-T-C		not specified	Uncertain significance (May 11, 2022)
16-68294740-C-T		not specified	Uncertain significance (Sep 09, 2021)
16-68294787-G-C		not specified	Uncertain significance (Dec 20, 2022)
16-68296494-A-G			Likely benign (Apr 10, 2018)
16-68296499-C-T		not specified	Uncertain significance (Jan 12, 2024)
16-68296659-A-G		not specified	Uncertain significance (Feb 07, 2023)
16-68296727-T-C			Benign (Apr 16, 2018)
16-68296780-C-T		not specified	Uncertain significance (Feb 22, 2023)
16-68296805-T-C		not specified	Uncertain significance (Feb 23, 2023)
16-68297268-T-C		SLC7A6-related disorder	Likely benign (Oct 28, 2019)
16-68297272-G-A		not specified	Uncertain significance (Jul 28, 2021)
16-68297276-T-C		not specified	Uncertain significance (Dec 15, 2023)
16-68301286-C-A		not specified	Uncertain significance (May 15, 2023)
16-68302405-T-C		not specified	Uncertain significance (Oct 17, 2023)
16-68302421-G-C		not specified	Uncertain significance (Sep 01, 2023)
16-68302437-T-C		not specified	Uncertain significance (Jan 30, 2024)
16-68302471-A-G		Epilepsy, progressive myoclonic, 12	Uncertain significance (Jun 23, 2021)
16-68304034-A-G		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A6OS	protein_coding	protein_coding	ENST00000263997	5	26444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.168	0.830	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.178	175	182	0.963	0.00000930	1987
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000122
Ashkenazi Jewish	0.000107	0.0000992
East Asian	0.000164	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.125
• hipred: Y
• hipred_score: 0.572
• ghis: 0.413

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a6os

Zebrafish Information Network

• Gene name: slc7a6os
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: immobile

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;protein transport;developmental process
• Cellular component: nucleus;cytoplasm