NM_032444.3:c.5242C>T

SLX4 · NP_115820.2:p.(Gln1748Ter) · NM_032444.3

GRCh37: chr16:3632606 G>A · GRCh38: chr16:3582605 G>A

Gene: SLX4 Transcript: NM_032444.3

Final call

VUS

PVS1 moderate PM1 moderate PM2 supporting

Variant details

Gene

SLX4

Transcript

NM_032444.3

Protein

NP_115820.2:p.(Gln1748Ter)

gnomAD AF

1.9212986491411174e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_032444.3:c.5242C>T (p.Gln1748Ter) is a nonsense variant in the terminal exon of SLX4, predicted to produce a truncated protein lacking the C-terminal 87 amino acids within the SLX1-binding domain.

SLX4 loss of function is an established disease mechanism for Fanconi anemia subtype FA-P, meeting the PVS1 gene-level gate.

PVS1 is applied at moderate strength: the variant escapes NMD (terminal exon) but truncates a critical functional domain (SBD, residues 1632–1834), consistent with PMC6185798 guidance.

PM1 is met at moderate strength: the variant is located within the experimentally defined SLX1-binding domain (SBD/CCD, residues 1632–1834), a critical functional domain required for Holliday junction resolvase activity.

PM2 is met at supporting strength: the variant is extremely rare in population databases (gnomAD v2.1 AF = 0.0032%; v4.1 AF = 0.0019%), well below the 0.1% PM2 threshold, with zero homozygotes observed.

No variant-specific functional studies, segregation data, de novo observations, or expert panel classifications were identified. ClinVar reports this variant as Uncertain Significance (Variation ID 864196).

Overall, two moderate criteria (PVS1_moderate + PM1_moderate) and one supporting criterion (PM2_supporting) are met. Under generic ACMG/AMP 2015 combination rules, 2 moderate + 1 supporting criteria do not reach the 'likely pathogenic' threshold, which requires 3 moderate or 2 moderate + 2 supporting. The current evidence profile is consistent with a variant of uncertain significance (VUS), pending additional functional, segregation, or case-control data.

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_032444.3:c.5242C>T is a nonsense variant predicted to produce a truncated protein at p.Gln1748Ter (Q1748*). SLX4 loss of function is an established disease mechanism for Fanconi anemia subtype FA-P, and the gene passes the PVS1 gene-level gate. However, the variant is located in the terminal exon (exon 15 of 15), predicting escape from nonsense-mediated decay and production of a protein truncated by only 87 C-terminal amino acids (4.7% of the 1835-residue protein). The truncation removes the C-terminal ~50% of the SLX1-binding domain (SBD, residues 1632–1834), a functionally critical region required for SLX1 interaction and Holliday junction resolvase activity. Under PMC6185798 guidance for last-exon nonsense variants that escape NMD but disrupt a critical functional domain, PVS1 is applied at moderate strength.	pvs1_generic_framework PMID:19596235 PMID:19596236 PMID:21240275
PS1	Not met	PS1 requires the same amino acid change as an established pathogenic variant. No pathogenic or likely pathogenic ClinVar variant at p.Gln1748 was identified in the PM5 candidate search and no literature reports of a pathogenic missense at this codon were found.	clinvar pm5_candidates
PS2	Not met	PS2 requires a confirmed de novo occurrence with both maternity and paternity confirmed. No de novo data for NM_032444.3:c.5242C>T were identified in ClinVar, literature, or any other source.
PS3	Not met	PS3 requires well-established functional studies showing a damaging effect for the variant or a systematically characterized range that includes this position. While SLX4 functional domains are well-characterized in the literature (the SLX1-binding domain was mapped to residues 1632–1834 by PMID:19596235, and Holliday junction resolvase activity depends on the C-terminal CCD domain as shown in PMID:19596236), no variant-specific functional assay has been performed on p.Gln1748Ter. The published functional studies characterized domain-level interactions via truncation mapping, not systematic saturation mutagenesis or tiling screens covering position 1748. Domain-level inference from sparse testing qualifies for PM1, not PS3. In accordance with the PS3 calibration rules, domain-level evidence from a limited set of truncation constructs without systematic characterization of each individual residue in the range does not satisfy PS3.	PMID:19596235 PMID:19596236
PS4	Not met	PS4 requires a statistically significant enrichment of the variant in affected individuals compared to controls. No case-control data, cohort studies enumerating this variant, or significant patient counts were identified in ClinVar or the reviewed literature. The variant is present at very low frequency in gnomAD (AF ~0.003%) but no comparable affected-population frequency data exist.	clinvar gnomad_v2 gnomad_v4
PS5	N/A	PS5 is not a criterion defined in the standard ACMG/AMP 2015 framework (Richards et al., PMID:25741868). The standard pathogenic criteria are PVS1, PS1–PS4, PM1–PM6, and PP1–PP5. No VCEP/CSPEC framework overrides this for SLX4.	PMID:25741868
PM1	Met	The variant p.Gln1748Ter is located within the SLX1-binding domain (SBD) of SLX4, a well-characterized critical functional domain spanning residues 1632–1834. The SBD is the extreme C-terminal conserved domain (CCD) that is both necessary and sufficient for SLX1 interaction, and SLX1 binding is required for Holliday junction resolvase activity. Domain mapping was established by systematic co-immunoprecipitation truncation analysis in PMID:19596235 (Fekairi et al. 2009, Figure 2A,C) and PMID:19596236 (Svendsen et al. 2009, Figure 2B, 4E). The nonsense variant truncates the protein within this domain, removing the C-terminal 87 amino acids and disrupting the conserved SBD. No benign missense variation has been observed in this domain in population databases at appreciable frequency. PM1 is met at moderate strength based on location in an experimentally defined, functionally critical protein domain whose disruption is consistent with the established loss-of-function disease mechanism.	PMID:19596235 PMID:19596236 gnomad_v2 gnomad_v4
PM2	Met	NM_032444.3:c.5242C>T is absent from or observed at extremely low frequency in large population databases. In gnomAD v2.1, the allele frequency is 3.20 × 10⁻⁵ (0.0032%, 9/281,628 alleles, 0 homozygotes) with grpmax filtering AF of 2.31 × 10⁻⁵. In gnomAD v4.1, the AF is 1.92 × 10⁻⁵ (0.0019%, 31/1,613,492 alleles, 0 homozygotes) with grpmax FAF of 1.45 × 10⁻⁵. The highest subpopulation frequency is in the Finnish population (AF = 8.09 × 10⁻⁵ in v2.1; 7.89 × 10⁻⁵ in v4.1). All observed frequencies are well below the 0.1% PM2 threshold for non-VCEP generic ACMG adjudication. No homozygotes are observed, consistent with a rare pathogenic variant in a gene where biallelic LoF causes Fanconi anemia.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a different pathogenic missense variant at the same amino acid residue. The variant p.Gln1748Ter is a nonsense change, not a missense. Furthermore, the automated PM5 candidate search found zero ClinVar variants at codon 1748 with any pathogenic classification, and classic same-residue PM5 semantics could not be confirmed. As a terminal truncation near the C-terminus rather than a missense at a residue with a known pathogenic alternative, PM5 does not apply.	pm5_candidates
PM6	Not met	PM6 requires a de novo observation without confirmation of paternity and maternity. No de novo reports for NM_032444.3:c.5242C>T were identified in ClinVar submissions, literature, or any other reviewed source.
PP1	Not met	PP1 requires cosegregation of the variant with disease in multiple affected family members. No segregation data are available for this variant in ClinVar or the reviewed literature.
PP2	N/A	PP2 applies to missense variants in genes where missense variation is a known disease mechanism and benign missense variation is rare. NM_032444.3:c.5242C>T is a nonsense (truncating) variant, not a missense variant. PP2 is not applicable.
PP3	Not met	PP3 requires multiple lines of computational evidence supporting a deleterious effect on the gene or gene product. SpliceAI predicts no significant splicing impact (max delta score = 0.02). REVEL score is not available for this variant. BayesDel score is 0.34181, which exceeds the recommended threshold of 0.27 for a deleterious prediction but is in a borderline range and represents only a single in silico predictor. HCI prior is not available for SLX4. With only one predictive tool providing a borderline score and SpliceAI showing no splicing effect, the multiple lines of computational evidence required for PP3 are not met.	spliceai bayesdel
PP4	Not met	PP4 requires the variant to be identified in a patient whose phenotype or family history is highly specific for a disease with a single genetic etiology. No patient-specific phenotype data are available for this variant in ClinVar or the reviewed literature. The ClinVar submissions do not include detailed phenotype information.	clinvar
PP5	Not met	PP5 requires a reputable source (e.g., clinical laboratory with recognized expertise) to have recently reported the variant as pathogenic. In ClinVar, NM_032444.3:c.5242C>T is classified as Uncertain Significance by all three submitting laboratories (Fulgent Genetics, Labcorp/Invitae, University of Chicago). The review status is 'criteria provided, single submitter' (not expert panel). Under the global PP5 rule requiring ClinVar 3-star expert panel classification, this variant does not meet the threshold. No expert panel has reviewed this variant.	clinvar
BA1	Not met	BA1 requires allele frequency >1% in any population database. gnomAD v2.1 AF = 0.0032% (9/281,628), v4.1 AF = 0.0019% (31/1,613,492). The highest subpopulation AF is 0.0081% in Finnish (v2.1). All observed frequencies are orders of magnitude below the 1% BA1 threshold.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 requires allele frequency >0.3% (non-VCEP generic ACMG threshold). gnomAD v2.1 AF = 0.0032%, v4.1 AF = 0.0019%, with highest subpopulation AF of 0.0081% (Finnish). All observed frequencies are far below the 0.3% threshold.	gnomad_v2 gnomad_v4
BS2	Not met	BS2 requires observation of the variant in a healthy adult in the homozygous state, or in trans with a pathogenic variant for a fully penetrant dominant disorder. No homozygotes are observed in gnomAD v2.1 (0/281,628) or v4.1 (0/1,613,492). No such observations were reported in ClinVar or the reviewed literature.	gnomad_v2 gnomad_v4
BS3	Not met	BS3 requires well-established functional studies showing no deleterious effect. No functional studies testing NM_032444.3:c.5242C>T specifically have been performed. The domain-level functional characterization of SLX4 (PMID:19596235, PMID:19596236) demonstrated that the C-terminal SBD/CCD domain is critical for SLX1 binding and HJ resolvase activity, which is consistent with a deleterious effect of truncation within this domain rather than a benign effect.	PMID:19596235 PMID:19596236
BS4	Not met	BS4 requires lack of segregation of the variant with disease in affected family members. No segregation data are available for this variant in any reviewed source.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. NM_032444.3:c.5242C>T is itself a truncating (nonsense) variant, not a missense variant. BP1 is therefore not applicable.
BP2	Not met	BP2 requires observation in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant. SLX4-associated disease (Fanconi anemia) is autosomal recessive. No co-occurrence data in trans or cis are available for this variant.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product. SpliceAI predicts no splicing impact (max delta = 0.02), satisfying one line of benign computational evidence. However, BayesDel scores the variant at 0.34181, exceeding the pathogenic threshold of 0.27 and contradicting a benign prediction. With conflicting in silico evidence (one benign, one deleterious), the requirement for multiple concordant lines of benign computational evidence is not met.	spliceai bayesdel
BP5	Not met	BP5 requires the variant to be found in a case with an alternate molecular basis for disease. No such data are available for this variant in ClinVar or the reviewed literature.
BP6	Not met	BP6 requires a reputable source to report the variant as benign. ClinVar classification is Uncertain Significance (Variation ID 864196) from all three submitting laboratories. No source reports this variant as benign or likely benign.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. NM_032444.3:c.5242C>T is a nonsense (stop-gain) variant, not a synonymous variant. BP7 is not applicable.	spliceai
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions; not applicable to a substitution variant.
PM3	N/A	PM3 requires observation in trans with a pathogenic variant; no phase data available for this variant.
PM4	N/A	PM4 applies to in-frame deletions/insertions or stop-loss variants; not applicable to a nonsense substitution variant.

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