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.517G>A (p.Val173Ile)

CA10524682

512592 (ClinVar)

Gene: SLC9A6

Condition: Christianson syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 8392c0c2-b085-4ae9-9c28-847604704552

HGVS expressions

NM_001379110.1:c.517G>A

NM_001379110.1(SLC9A6):c.517G>A (p.Val173Ile)

NC_000023.11:g.135998551G>A

CM000685.2:g.135998551G>A

NC_000023.10:g.135080710G>A

CM000685.1:g.135080710G>A

NC_000023.9:g.134908376G>A

NG_017160.1:g.18125G>A

ENST00000370695.8:c.673G>A

ENST00000370701.6:c.517G>A

ENST00000630721.3:c.517G>A

ENST00000636092.1:c.517G>A

ENST00000636347.1:c.517G>A

ENST00000637195.1:c.421G>A

ENST00000637234.1:c.517G>A

ENST00000637581.1:c.517G>A

ENST00000643775.1:n.460G>A

ENST00000674809.1:c.460G>A

ENST00000675550.1:n.458G>A

ENST00000675856.1:n.460G>A

ENST00000676043.1:c.460G>A

ENST00000678163.1:c.673G>A

ENST00000370695.6:c.673G>A

ENST00000370698.7:c.577G>A

ENST00000370701.5:c.517G>A

ENST00000627534.2:c.517G>A

NM_001042537.1:c.673G>A

NM_001177651.1:c.517G>A

NM_006359.2:c.577G>A

NM_001330652.1:c.421G>A

NM_001177651.2:c.517G>A

NM_001330652.2:c.421G>A

NM_006359.3:c.577G>A

NM_001042537.2:c.673G>A

NM_001400909.1:c.517G>A

NM_001400910.1:c.517G>A

NM_001400911.1:c.517G>A

NM_001400912.1:c.517G>A

NM_001400913.1:c.421G>A

Likely Benign

BS2_Supporting BS1 BP5 BP4

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.Val193Ile variant in SLC9A6 (NM_006359.2) is 0.008% in South Asian sub population in gnomAD v4, 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). Computational analysis prediction tools suggest that the p.Val193Ile variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). The p.Val193Ile variant is observed in the hemizygous state in at least 1 unaffected individuals (internal database - GeneDx) (BS2_supporting). The p.Val193Ile variant is found in a patient with an alternate molecular basis of disease (internal database - GeneDx) (BP5). In summary, the p.Val193Ile variant in SLC9A6 is classified as likely benign based on the ACMG/AMP criteria (BS1, BP4, BS2_supporting, BP5).

BS2_Supporting

The p.Val193Ile variant is observed in the hemizygous state in at least 1 unaffected individuals (internal database - GeneDx) (BS2_supporting).

BS1

BP5

The p.Val193Ile variant is found in a patient with an alternate molecular basis of disease (internal database - GeneDx) (BP5).

BP4

Computational analysis prediction tools suggest that the p.Val193Ile variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4).

Approved on: 2024-02-23

Published on: 2024-03-31

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