Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001379110.1(SLC9A6):c.516C>T (p.Phe172=)

CA518744234

469637 (ClinVar)

Gene: SLC9A6
Condition: Christianson syndrome
Inheritance Mode: X-linked inheritance (dominant (HP:0001423))
Link to MONDO
UUID: 80930d02-04a4-47cd-bd49-a427b39b4670

HGVS expressions

NM_001379110.1:c.516C>T
NM_001379110.1(SLC9A6):c.516C>T (p.Phe172=)
NC_000023.11:g.135998550C>T
CM000685.2:g.135998550C>T
NC_000023.10:g.135080709C>T
CM000685.1:g.135080709C>T
NC_000023.9:g.134908375C>T
NG_017160.1:g.18124C>T
ENST00000370695.8:c.672C>T
ENST00000370701.6:c.516C>T
ENST00000630721.3:c.516C>T
ENST00000636092.1:c.516C>T
ENST00000636347.1:c.516C>T
ENST00000637195.1:c.420C>T
ENST00000637234.1:c.516C>T
ENST00000637581.1:c.516C>T
ENST00000643775.1:n.459C>T
ENST00000674809.1:c.459C>T
ENST00000675550.1:n.457C>T
ENST00000675856.1:n.459C>T
ENST00000676043.1:c.459C>T
ENST00000678163.1:c.672C>T
ENST00000370695.6:c.672C>T
ENST00000370698.7:c.576C>T
ENST00000370701.5:c.516C>T
ENST00000627534.2:c.516C>T
NM_001042537.1:c.672C>T
NM_001177651.1:c.516C>T
NM_006359.2:c.576C>T
NM_001330652.1:c.420C>T
NM_001177651.2:c.516C>T
NM_001330652.2:c.420C>T
NM_006359.3:c.576C>T
NM_001042537.2:c.672C>T
NM_001400909.1:c.516C>T
NM_001400910.1:c.516C>T
NM_001400911.1:c.516C>T
NM_001400912.1:c.516C>T
NM_001400913.1:c.420C>T

Likely Benign

Met criteria codes 4
PM2_Supporting BS2 BP4 BP7

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The p.Phe192= variant in SLC9A6 (NM_006359.2) is observed in the hemizygous state in at least 3 unaffected individuals (internal database - GeneDx) (BS2). The p.Phe172= variant in SLC9A6 is absent from gnomAD (PM2_Supporting). The silent p.Phe172= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7). In the absence of other pathogenic evidence beyond PM2_Supporting, and because this variant has been observed in 3 unaffected hemizygous individuals, the ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel has agreed to overrule the PM2_Supporting criterion and classified the p.Phe192= variant in SLC9A6 as Likely Benign (BS2, BP4, BP7).
Met criteria codes
PM2_Supporting
The p.Phe192= variant in SLC9A6 is absent from gnomAD (PM2_supporting).
BS2
The p.Phe192= variant is observed in at least 3 unaffected individuals (internal database - GeneDx) (BS2).
BP4
The silent p.Phe192= 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.Phe192= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide
Approved on: 2023-10-13
Published on: 2023-12-11
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