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]
Link to SEPIO compliant JSON-LD document
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_001379110.1(SLC9A6):c.452A>T (p.His151Leu)

CA318501

207233 (ClinVar)

Gene: SLC9A6
Condition: Christianson syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 5974f478-85f5-43f6-bf7d-83ca0a12a1f4

HGVS expressions

NM_001379110.1:c.452A>T
NM_001379110.1(SLC9A6):c.452A>T (p.His151Leu)
NC_000023.11:g.135998486A>T
CM000685.2:g.135998486A>T
NC_000023.10:g.135080645A>T
CM000685.1:g.135080645A>T
NC_000023.9:g.134908311A>T
NG_017160.1:g.18060A>T
ENST00000370695.8:c.608A>T
ENST00000370701.6:c.452A>T
ENST00000630721.3:c.452A>T
ENST00000636092.1:c.452A>T
ENST00000636347.1:c.452A>T
ENST00000637195.1:c.356A>T
ENST00000637234.1:c.452A>T
ENST00000637581.1:c.452A>T
ENST00000643775.1:n.395A>T
ENST00000674809.1:c.395A>T
ENST00000675550.1:n.393A>T
ENST00000675856.1:n.395A>T
ENST00000676043.1:c.395A>T
ENST00000678163.1:c.608A>T
ENST00000370695.6:c.608A>T
ENST00000370698.7:c.512A>T
ENST00000370701.5:c.452A>T
ENST00000627534.2:c.452A>T
NM_001042537.1:c.608A>T
NM_001177651.1:c.452A>T
NM_006359.2:c.512A>T
NM_001330652.1:c.356A>T
NM_001177651.2:c.452A>T
NM_001330652.2:c.356A>T
NM_006359.3:c.512A>T
NM_001042537.2:c.608A>T
NM_001400909.1:c.452A>T
NM_001400910.1:c.452A>T
NM_001400911.1:c.452A>T
NM_001400912.1:c.452A>T
NM_001400913.1:c.356A>T

Likely Benign

Met criteria codes 2
BS2 BP5
Not Met criteria codes 2
PM2 BS1

Evidence Links 0

Expert Panel

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 p.His171Leu variant in SLC9A6 (NM_006359.2) is present in 14 XX and 6 XY individual(s) in gnomAD v4.0 (0.002%) (not sufficient to meet BS1 criteria). The p.His171Leu variant is observed in at least 2 unaffected individuals (GeneDx internal database) (BS2). The p.His171Leu variant is found in a patient with an alternate molecular basis of disease (GeneDx internal database) (BP5). In summary, the p.His171Leu variant in SLC9A6 is classified as likely benign based on the ACMG/AMP criteria (BS2, BP5).
Met criteria codes
BS2
The p.His171Leu variant is observed in at least 2 unaffected individuals (GeneDx internal database).
BP5
The p.His171Leu variant is found in a patient with an alternate molecular basis of disease (GeneDx internal database).
Not Met criteria codes
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The p.His171Leu variant in SLC9A6 is present in 14 XX and 6 XY individual(s) in gnomAD v4.0 (0.002%) (not sufficient to meet BS1 criteria).
Approved on: 2024-04-18
Published on: 2024-07-01
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