Variant Report |

Variant classification summary

ATRX · NP_000480.3:p.? · NM_000489.5

GRCh37: chrX:76949427 C>T · GRCh38: chrX:77693938 C>T

Gene: ATRX Transcript: NM_000489.5

Final call

Variant details

Gene

ATRX

Transcript

NM_000489.5

Protein

NP_000480.3:p.?

gnomAD AF

ClinVar

Likely pathogenic

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000489.5:c.371-1G>A disrupts the canonical splice acceptor site at intron 5 of ATRX, a gene in which germline loss of function is an established mechanism for ATR-X syndrome (MIM #301040). Under the ClinGen SVI PVS1 recommendations (PMC6185798), this qualifies for PVS1 at very strong strength.

2

The variant is absent from gnomAD-Canada v1.0 and independently reported as absent from population databases by the submitting clinical laboratory (Labcorp Genetics/Invitae). This rarity, combined with its location on the X chromosome in a gene causing an X-linked disorder, meets PM2 at moderate strength.

3

SpliceAI predicts complete acceptor loss (max delta 0.99, DS_AL 0.99), consistent with the predicted loss-of-function effect. Per PMC6185798, PP3 is not stacked with PVS1 for the same splice prediction evidence.

4

No variant-specific functional data (PS3), de novo reports (PS2/PM6), segregation data (PP1), or proband phenotype details (PP4) are available in the case materials. ClinVar classification is from a single submitter (1-star) and does not meet PP5 threshold.

5

Combined ACMG evidence: PVS1 (very strong) + PM2 (moderate). Under generic ACMG/AMP 2015 combination rules, one very strong and one moderate criterion yields a classification of Likely Pathogenic.

Final determination:

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	This variant disrupts the canonical splice acceptor site at intron 5 of ATRX (c.371-1G>A, ±1 position). ATRX loss of function is an established disease mechanism for ATR-X syndrome (alpha-thalassemia/mental retardation syndrome, X-linked, MIM #301040), supported by germline disease literature. Under the ClinGen SVI PVS1 decision tree (PMC6185798), canonical ±1,2 splice site variants in genes with a validated germline loss-of-function mechanism qualify for PVS1 at full strength. SpliceAI predicts near-complete acceptor loss (delta score 0.99), consistent with aberrant splicing and a predicted null effect.	pvs1_generic_framework pvs1_gene_context pvs1_variant_assessment spliceai
PS1	N/A	Intronic splice site variant; no missense comparator at the same residue position is applicable.
PS2	Not assessed	No de novo data available for this variant in the case materials.
PS3	Not met	No variant-specific functional data identified for NM_000489.5:c.371-1G>A. The available literature discusses ATRX mutations at the gene level but does not report experimental functional characterization of this specific splice variant. PMID:23681356 describes brain MRI findings in 27 ATR-X patients but provides no functional assay data for c.371-1G>A. PMID:36496321 describes genetic testing results in hypospadias patients without functional characterization. No experimental evidence (luciferase, splicing assay, RNA analysis, or protein studies) was found for this variant.
PS4	Not assessed	Insufficient proband count data. The variant is reported in ClinVar by a single clinical laboratory (Labcorp Genetics/Invitae) as Likely pathogenic, but individual case counts and detailed phenotype descriptions are not available in the case materials. No case-control enrichment data is present.	clinvar
PS5	N/A	Intronic splice site variant; PS5 requires a different pathogenic nucleotide change at the same codon producing a different amino acid substitution. This semantics is not applicable to splice site variants.
PM1	Not assessed	Insufficient information to determine whether this splice site falls within a critical functional domain or established mutational hotspot in ATRX. The variant disrupts the splice acceptor of intron 5 (exon 6 boundary). Cancerhotspots.org did not identify a significant hotspot at the affected region, and available literature does not provide domain-level characterization specific to this splice junction. PM1 is not applied at this time.
PM2	Met	This variant is absent from gnomAD-Canada v1.0. gnomAD v2.1 and v4.1 population frequency data were unavailable due to query timeout, but the clinical laboratory submission (Invitae) independently confirmed absence from population databases. As a canonical splice site variant on the X chromosome causing a well-established X-linked disorder, standing population variation is expected to be exceedingly low. The combined evidence supports rarity consistent with PM2 at moderate strength under generic ACMG/AMP 2015.	gnomad_canada clinvar
PM5	N/A	Intronic splice site variant with no protein residue context; PM5 requires a different pathogenic missense change at the same residue, which is not applicable to splice site variants. The automated PM5 candidate harvest also returned no candidates.	pm5_candidates
PM6	Not assessed	No de novo data available for this variant. PM6 requires confirmation of de novo occurrence with confirmed maternity and paternity.
PP1	Not assessed	No segregation data available in the case materials. PP1 requires cosegregation of the variant with disease in multiple affected family members.
PP2	N/A	Splice site (non-missense) variant; PP2 applies only to missense variants in genes where missense variants are a common disease mechanism and benign missense variation is low. Not applicable to this variant type.
PP3	N/A	Canonical splice site variant with PVS1 already applied. Per ClinGen SVI PVS1 recommendations (PMC6185798), PP3 should not be stacked with PVS1 for the same splice-effect prediction evidence. SpliceAI predicts a deleterious effect (max delta 0.99, acceptor loss 0.99) and BayesDel adds deleterious at 0.83, but this in silico evidence is already captured by the PVS1 assessment of the splice disruption.	spliceai bayesdel pvs1_generic_framework
PP4	Not assessed	No proband phenotype data available in the case materials for specificity assessment. PP4 requires that the proband's phenotype or family history is highly specific for the disease associated with the gene.
PP5	Not met	ClinVar entry (variation ID 1067789) classifies this variant as Likely pathogenic under a single submitter (Labcorp Genetics/Invitae) with review status 'criteria provided, single submitter' (1-star). PP5 requires a pathogenic classification from a reputable source, typically an expert panel (3-star) or multiple concordant submitters. A single 1-star submission does not meet the PP5 threshold under generic ACMG/AMP 2015. Additionally, the ClinVar record is cataloged under NM_000489.6:c.485-1G>A (different transcript version), flagged as 'no_exact_match' by the pipeline, adding further uncertainty to direct citation.	clinvar
BA1	Not met	This variant is absent from gnomAD-Canada v1.0. The allele frequency does not exceed the 1% threshold required for BA1.	gnomad_canada
BS1	Not met	This variant is absent from gnomAD-Canada v1.0. The allele frequency does not exceed the 0.3% threshold required for BS1.	gnomad_canada
BS2	Not assessed	No data available on observation of this variant in healthy adult controls. BS2 requires documented observation in a healthy adult individual, particularly for fully penetrant disorders.
BS3	Not assessed	No functional studies demonstrating a neutral or benign effect for this variant are available. BS3 requires well-established in vitro or in vivo functional studies showing no damaging effect on protein function or splicing.
BS4	Not assessed	No segregation data available demonstrating lack of cosegregation with disease. BS4 requires observation that the variant does not segregate with disease in affected family members.
BP1	N/A	Splice site (predicted truncating/non-missense) variant; BP1 applies to missense variants in genes where truncating variants are the primary known disease mechanism. Not applicable to this variant type.
BP2	Not assessed	No data available on observation of this variant in trans with a known pathogenic variant. BP2 requires documented co-occurrence in trans with a pathogenic variant in a gene associated with a recessive disorder.
BP4	Not met	Multiple in silico tools predict a deleterious effect rather than a benign effect. SpliceAI predicts complete acceptor loss (max delta 0.99, DS_AL 0.99) and BayesDel returns a deleterious score of 0.83. These predictions are inconsistent with a benign interpretation under BP4.	spliceai bayesdel
BP5	Not assessed	No data available on a case with this variant where an alternative molecular basis for disease was identified. BP5 requires that the variant is observed in a case with an alternate molecular cause.
BP6	Not met	The only ClinVar classification for this variant is Likely pathogenic (not benign or likely benign). BP6 requires a reputable source to report the variant as benign. No benign classification exists in ClinVar.	clinvar
BP7	N/A	Splice site variant with strong splice effect predictions. BP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact on the splice consensus sequence. This variant directly disrupts the canonical splice acceptor consensus, so BP7 does not apply.	spliceai
BP3	N/A	Skipped per directive — this is a splice site variant, not an in-frame indel in a repetitive region.
PM3	N/A	Skipped per directive — ATR-X syndrome is X-linked, not recessive; PM3 (in trans with pathogenic variant) does not apply.
PM4	N/A	Skipped per directive — this is a splice site variant, not an in-frame deletion/insertion or stop-loss variant.

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