Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

Variant: NM_001379110.1(SLC9A6):c.1083G>A (p.Leu361=)

CA10524772

469632 (ClinVar)

Gene: SLC9A6

Condition: Christianson syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 83d8c4a4-679b-424d-bc07-259435d6b659

Approved on: 2024-02-23

Published on: 2024-03-31

HGVS expressions

NM_001379110.1:c.1083G>A

NM_001379110.1(SLC9A6):c.1083G>A (p.Leu361=)

NC_000023.11:g.136016647G>A

CM000685.2:g.136016647G>A

NC_000023.10:g.135098806G>A

CM000685.1:g.135098806G>A

NC_000023.9:g.134926472G>A

NG_017160.1:g.36221G>A

ENST00000370695.8:c.1239G>A

ENST00000370701.6:c.1083G>A

ENST00000630721.3:c.1083G>A

ENST00000636092.1:c.1083G>A

ENST00000636347.1:c.1083G>A

ENST00000636798.1:n.518G>A

ENST00000637195.1:c.987G>A

ENST00000637234.1:c.1083G>A

ENST00000637581.1:c.1083G>A

ENST00000643775.1:n.1026G>A

ENST00000675856.1:n.1026G>A

ENST00000678163.1:c.1239G>A

ENST00000370695.6:c.1239G>A

ENST00000370698.7:c.1143G>A

ENST00000370701.5:c.1083G>A

NM_001042537.1:c.1239G>A

NM_001177651.1:c.1083G>A

NM_006359.2:c.1143G>A

NM_001330652.1:c.987G>A

NM_001177651.2:c.1083G>A

NM_001330652.2:c.987G>A

NM_006359.3:c.1143G>A

NM_001042537.2:c.1239G>A

NM_001400909.1:c.1083G>A

NM_001400910.1:c.1083G>A

NM_001400911.1:c.1083G>A

NM_001400912.1:c.1083G>A

NM_001400913.1:c.987G>A

Benign

BP4 BP7 BP5_Strong BS2 BS1

Evidence Links 0

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC9A6 Version 3.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The allele frequency of the p.Leu381= variant in SLC9A6 (NM_006359.2) is 0.024% in European (Non-Finnish) sub population in gnomAD v2, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The silent p.Leu381= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7). The p.Leu381= variant is observed in the hemizygous state in at least 2 unaffected individuals (internal database - GeneDx) (BS2_strong). The p.Leu381= variant is found in at least 3 patients with an alternate molecular basis of disease (internal database - GeneDx, internal database - Invitae) (BP5_strong). In summary, the p.Leu381= variant in SLC9A6 is classified as benign based on the ACMG/AMP criteria (BS1, BP4, BP7, BS2_strong, BP5_strong).

BP4

The silent p.Leu381=variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7).

BP7

The silent p.Leu381=variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7).

BP5_Strong

The p.Leu381= variant is found in at least 3 patients with an alternate molecular basis of disease (internal database - GeneDx, internal database - Invitae) (BP5_Strong).

BS2

The p.Leu381= variant is observed in the hemizygous state in at least 2 unaffected individuals (internal database - GeneDx) (BS2_Strong).

BS1

The allele frequency of the p.Leu381= variant in SLC9A6 (NM_006359.2) is 0.024% in European (non-Finnish) sub population in gnomAD v2, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1).

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