Evidence Repository
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Variant: NM_001042537.1(SLC9A6):c.526-9_526-5del

CA318538

207248 (ClinVar)

Gene: SLC9A6
Condition: Christianson syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: db0297b9-0514-429a-a4f0-7933c2cd4d05
Approved on: 2022-02-18
Published on: 2022-06-30

HGVS expressions

NM_001042537.1:c.526-9_526-5del
NM_001042537.1(SLC9A6):c.526-9_526-5del
NC_000023.11:g.135998099_135998103del
CM000685.2:g.135998099_135998103del
NC_000023.10:g.135080258_135080262del
CM000685.1:g.135080258_135080262del
NC_000023.9:g.134907924_134907928del
NG_017160.1:g.17673_17677del
ENST00000370695.8:c.526-9_526-5del
ENST00000370701.6:c.370-9_370-5del
ENST00000630721.3:c.370-9_370-5del
ENST00000636092.1:c.370-9_370-5del
ENST00000636347.1:c.370-9_370-5del
ENST00000637195.1:c.274-9_274-5del
ENST00000637234.1:c.370-9_370-5del
ENST00000637581.1:c.370-9_370-5del
ENST00000643775.1:n.313-9_313-5del
ENST00000674809.1:n.313-9_313-5del
ENST00000675550.1:n.311-9_311-5del
ENST00000675856.1:n.313-9_313-5del
ENST00000676043.1:n.313-9_313-5del
ENST00000678163.1:c.526-9_526-5del
ENST00000370695.6:c.526-9_526-5del
ENST00000370698.7:c.430-9_430-5del
ENST00000370701.5:c.370-9_370-5del
ENST00000627534.2:c.370-9_370-5del
NM_001177651.1:c.370-9_370-5del
NM_006359.2:c.430-9_430-5del
NM_001330652.1:c.274-9_274-5del
NM_001177651.2:c.370-9_370-5del
NM_001330652.2:c.274-9_274-5del
NM_006359.3:c.430-9_430-5del
NM_001042537.2:c.526-9_526-5del
NM_001379110.1:c.370-9_370-5del
NM_001400909.1:c.370-9_370-5del
NM_001400910.1:c.370-9_370-5del
NM_001400911.1:c.370-9_370-5del
NM_001400912.1:c.370-9_370-5del
NM_001400913.1:c.274-9_274-5del
NM_001379110.1(SLC9A6):c.370-9_370-5del
More

Pathogenic

Met criteria codes 5
PS2 PS3 PS4_Supporting PM2_Supporting PP1_Moderate
Not Met criteria codes 1
PVS1

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 c.430-9_430-5del variant in SLC9A6 occurs in the de novo state (biological parentage confirmed) in an individual with delayed motor milestones and hypotonia (Baylor Genetics internal database)(PS2). RNA study has shown that this variant impacts splicing (PMID 27256868) (PS3). This variant has been reported to segregate in four informative meioses (PMID 27256868)(PP1_moderate). The c.430-9_430-5del variant in SLC9A6 has been observed in 2 unrelated families with Christianson syndrome (PMID 27256868, Baylor Genetics internal database) (PS4_supporting). The c.430-9_430-5del variant in SLC9A6 is absent from gnomAD (PM2_supporting). In summary The c.430-9_430-5del variant in SLC9A6 is classified as pathogenic for Christianson syndrome based on the ACMG/AMP criteria (PS2, PS3, PP1_moderate, PS4_supporting, PM2_supporting).
Met criteria codes
PS2
The c.430-9_430-5del variant in SLC9A6 occurs in the de novo state (biological parentage confirmed) in an individual with delayed motor milestones and hypotonia (Baylor Genetics internal data).
PS3
RNA study has shown that this variant impacts splicing (PMID 27256868).
PS4_Supporting
The c.430-9_430-5del variant in SLC9A6 has been observed in 2 unrelated families with Christianson syndrome (PMID 27256868, Baylor Genetics internal database).
PM2_Supporting
The c.430-9_430-5del variant in SLC9A6 is absent from gnomAD.
PP1_Moderate
The c.430-9_430-5del variant in SLC9A6 has been reported to segregate in four informative meioses (PMID 27256868).
Not Met criteria codes
PVS1
Consulted ClinGen that experimentally confirmed LOF should be under PS3 not PVS1 for current guideline, but this will change in next guideline. But PS3 and PVS1 should not be applied simultaneously for this situation.
Curation History
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