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_001042537.1(SLC9A6):c.604-1G>A

CA180441

167702 (ClinVar)

Gene: SLC9A6

Condition: Christianson syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 217ba976-d6f6-4342-b89a-dec9dfc194f7

HGVS expressions

NM_001042537.1:c.604-1G>A

NM_001042537.1(SLC9A6):c.604-1G>A

ENST00000370695.8:c.604-1G>A

ENST00000370701.6:c.448-1G>A

ENST00000630721.3:c.448-1G>A

ENST00000636092.1:c.448-1G>A

ENST00000636347.1:c.448-1G>A

ENST00000637195.1:c.352-1G>A

ENST00000637234.1:c.448-1G>A

ENST00000637581.1:c.448-1G>A

ENST00000643775.1:n.391-1G>A

ENST00000674809.1:n.391-1G>A

ENST00000675550.1:n.389-1G>A

ENST00000675856.1:n.391-1G>A

ENST00000676043.1:n.391-1G>A

ENST00000678163.1:c.604-1G>A

ENST00000370695.6:c.604-1G>A

ENST00000370698.7:c.508-1G>A

ENST00000370701.5:c.448-1G>A

ENST00000627534.2:c.448-1G>A

NM_001177651.1:c.448-1G>A

NM_006359.2:c.508-1G>A

NM_001330652.1:c.352-1G>A

NM_001177651.2:c.448-1G>A

NM_001330652.2:c.352-1G>A

NM_006359.3:c.508-1G>A

NM_001042537.2:c.604-1G>A

NM_001379110.1:c.448-1G>A

NC_000023.11:g.135998481G>A

CM000685.2:g.135998481G>A

NC_000023.10:g.135080640G>A

CM000685.1:g.135080640G>A

NC_000023.9:g.134908306G>A

NG_017160.1:g.18055G>A

Pathogenic

PM2_Supporting PVS1 PP1_Moderate

Evidence Links 0

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The c.508-1G>A variant in SLC9A6 is predicted to affect a canonical splice site and lead to a truncated or absent protein in a gene where loss-of-function is an established mechanism. There is significant evidence that loss of this region of the gene is pathogenic (PVS1). The c.508-1G>A variant in SLC9A6 has been reported to segregate in three informative meioses (internal database) (PP1_moderate). This variant is absent from gnomAD (PM2_supporting). In summary, the c.508-1G>A variant in GENE is classified as Pathogenic for Christianson syndrome based on the ACMG/AMP criteria (PVS1, PP1_moderate, PM2_supporting).

PM2_Supporting

The c.508-1G>A variant in SLC9A6 is absent from gnomAD

PVS1

The c.508-1G>A variant in SLC9A6 is predicted to cause a premature stop codon that leads to a truncated or absent protein in a gene where loss-of-function is an established mechanism.

PP1_Moderate

The variant has been reported to segregate in three affected family males with intellectual disability and developmental delay (EGL data).

Approved on: 2021-03-02

Published on: 2021-05-07

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