Variant classification summary

NM_001015877.1:c.1003A>T

PHF6 · NP_001015877.1:p.(Arg335Ter) · NM_001015877.1

GRCh37: chrX:133559265 A>T · GRCh38: chrX:134425235 A>T

Gene: PHF6 Transcript: NM_001015877.1

Final call

VUS

PVS1 moderate PM2 supporting PP3 supporting

Variant details

Gene

PHF6

Transcript

NM_001015877.1

Protein

NP_001015877.1:p.(Arg335Ter)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_001015877.1:c.1003A>T (p.Arg335Ter) introduces a premature termination codon in PHF6, a gene in which loss of function causes Börjeson-Forssman-Lehmann syndrome (X-linked intellectual disability).

2

The nonsense variant lies in the terminal exon (exon 11/11) and removes only 31 C-terminal amino acids, consistent with predicted NMD escape; under PMC6185798, this is assigned PVS1 at Moderate strength.

3

The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting PM2 at Supporting strength.

4

BayesDel in silico prediction score of 0.83 supports a deleterious effect, meeting PP3 at Supporting strength.

5

The combination of PVS1_Moderate, PM2_Supporting, and PP3_Supporting yields 1 Moderate and 2 Supporting criteria. Under generic ACMG/AMP 2015 final combination rules (PMID:25741868), this does not meet the threshold for Likely Pathogenic (which requires ≥3 Moderate, or 1 Moderate + ≥4 Supporting, or a Strong criterion). The evidence is indeterminate and the variant is classified as a Variant of Uncertain Significance.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	NM_001015877.1:c.1003A>T introduces a premature termination codon at p.Arg335Ter (R335*) in PHF6, a gene in which loss of function is an established mechanism for Börjeson-Forssman-Lehmann syndrome (X-linked intellectual disability). However, the variant lies in the terminal exon (exon 11 of 11), and the truncation removes only 31 C-terminal amino acids (8.5% of the 366-residue protein), consistent with predicted NMD escape. The C-terminal region spanning residues 279–365 has been shown to be functionally important for neuronal migration (deletion 279–365 impairs migration in a mouse model), but the specific contribution of residues 335–365 is not independently established. Under PMC6185798, a nonsense variant in the last exon with an affected region of uncertain criticality is assigned PVS1_Moderate.	pvs1_generic_framework
PS1	N/A	No alternate nucleotide change at c.1003 has been reported in ClinVar or the literature; no same-site comparator exists.
PS2	Not assessed	No de novo occurrence data identified in any reviewed publication for NM_001015877.1:c.1003A>T.
PS3	Not assessed	No variant-specific functional assay for p.R335* was identified in the reviewed literature. PMID:23791194 tested a C-terminal deletion (279–365) encompassing this position but did not assess the p.R335* point variant. PMID:12676923 examined p.D333del, a different variant. PMID:27479181 had no accessible full text or abstract. OncoKB assigns Likely Oncogenic to R335* in a somatic context, but this is a curated gateway annotation and does not constitute independent germline functional evidence.
PS4	Not assessed	The variant is absent from ClinVar and no case reports were identified in the reviewed literature. No prevalence or case-control data available.
PS5	Not assessed	No information about parental testing or defined inheritance pattern for this variant.
PM1	Not met	The variant lies in the C-terminal region (residue 335) of PHF6, outside the two characterized PHD finger domains. While the C-terminal region (279–365) has been shown to contribute to neuronal migration function in a broad deletion context (PMID:23791194), this region has not been established as a well-defined mutational hotspot or critical functional domain with a high concentration of pathogenic missense variants, as required by PM1.
PM2	Met	NM_001015877.1:c.1003A>T is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, consistent with a rare variant not observed in large population cohorts.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No same-residue comparator missense variants classified as pathogenic were identified in ClinVar; PM5 candidate harvesting found zero eligible comparators.
PM6	Not assessed	No de novo event reported for this variant in the reviewed literature.
PP1	Not assessed	No cosegregation data available for this variant.
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation; NM_001015877.1:c.1003A>T is a nonsense variant.
PP3	Met	BayesDel score of 0.83 predicts a damaging effect for this substitution. SpliceAI predicts no significant splice alteration (max delta score 0.07), consistent with the variant's primary consequence being at the protein level via premature termination.	bayesdel spliceai
PP4	Not assessed	No patient phenotype data specific to this variant are available.
PP5	Not met	This variant is absent from ClinVar and has not been classified by any expert panel or reputable clinical source.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada; allele frequency is 0%, far below the BA1 threshold of 1%.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from gnomAD; allele frequency is 0%, below the BS1 threshold of 0.3%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	N/A	PHF6 is X-linked; observation in a healthy hemizygous male would be informative for BS2 but this criterion is not assessable absent such data, and the typical autosomal homozygous framework does not apply.
BS3	Not met	No variant-specific functional study demonstrates a benign or neutral effect for p.R335*. The C-terminal deletion tested in PMID:23791194 (residues 279–365) showed impaired function, which is consistent with a deleterious rather than benign effect.
BS4	Not assessed	No segregation data available to assess lack of cosegregation with disease.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease; NM_001015877.1:c.1003A>T is a nonsense (truncating) variant.
BP2	N/A	BP2 (observation in trans with a pathogenic variant) is not applicable to X-linked PHF6.
BP4	Not met	BayesDel score of 0.83 predicts a damaging effect. SpliceAI max delta score of 0.07 indicates no cryptic splicing, but this does not constitute benign computational evidence when the primary variant consequence (nonsense) is inherently deleterious.	bayesdel spliceai
BP5	Not assessed	No observation of this variant in a case with an alternate molecular basis for disease.
BP6	N/A	No reputable source has classified this variant as benign; the variant is absent from ClinVar entirely, so BP6 cannot be applied.
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact; NM_001015877.1:c.1003A>T is a nonsense variant.

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