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TAF1
Final classification
VUS
TAF1 c.3811_3812delinsCC · p.Lys1271Pro
TAF1

NM_004606.4:c.3811_3812delinsCC (p.Lys1271Pro) is an in-frame deletion-insertion in TAF1 resulting in a missense substitution at codon 1271.

Gene
TAF1
Transcript
NM_004606.4
HGVS · transcript:coding
NM_004606.4:c.3811_3812delinsCC
Consequence
N/A
GRCh38
chrX:71398702 AA>CC
GRCh37
chrX:70618552 AA>CC
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate; combination = 1 moderate, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate; combination = 1 moderate, which maps to VUS.
Classification rationale
PM2 VUS
TAF1 c.3811_3812delinsCC

NM_004606.4:c.3811_3812delinsCC (p.Lys1271Pro) is an in-frame deletion-insertion in TAF1 resulting in a missense substitution at codon 1271. This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, meeting PM2 at moderate strength.1 The variant is absent from ClinVar, providing no external pathogenic or benign classification.2 No variant-specific functional data, segregation data, de novo reports, or case-control studies are available for this variant. In silico splice prediction (SpliceAI max delta 0.01) suggests no splicing impact; REVEL and BayesDel are not applicable to this indel variant.3 TAF1 loss of function is an established disease mechanism (X-linked dystonia-parkinsonism via SVA retrotransposon insertion, and missense variants cause X-linked syndromic intellectual disability MRXS33); however, this variant is a missense change, not a null variant, so PVS1 does not apply. Overall, only one moderate pathogenic criterion (PM2) is met. Per generic ACMG/AMP 2015 combination rules, a single moderate criterion is insufficient for classification as likely pathogenic; the variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 VUS
Gene diagram · NM_004606.4 · variants mapped to exon structure
TAF1 NM_004606.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 24 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
NM_004606.4:c.3811_3812delinsCC is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 population databases. This absence supports pathogenicity under generic ACMG/AMP PM2 at moderate strength.
Absent from gnomAD v2.1 (exomes).Absent from gnomAD v4.1 (exomes).Absent from gnomAD-Canada v1.0 (genomes).
Assessed · not applied
Pathogenic
PVS1 NM_004606.4:c.3811_3812delinsCC results in an in-frame deletion-insertion (p.Lys1271Pro), which is a missense substitution, not a null variant.
PS1 No alternative nucleotide change resulting in the same amino acid substitution (Lys1271Pro) has been reported as pathogenic.
PS2 No de novo occurrence data with confirmed paternity and maternity is available for this variant.
PS3 No variant-specific or systematic range functional data is available for NM_004606.4:c.3811_3812delinsCC (p.Lys1271Pro).
PS4 No case-control data or statistical evidence demonstrating enrichment of this variant in affected individuals versus controls is available.
PM1 Residue 1271 does not lie within a statistically significant mutational hotspot per cancerhotspots.org.
PM6 No de novo occurrence (without confirmed paternity and maternity) has been reported for this variant.
PP1 No co-segregation data in multiple affected family members is available for this variant.
PP2 No constraint metrics (Z-score, missense depletion) for TAF1 are available to determine a low rate of benign missense variation.
PP3 In silico prediction tools (REVEL, BayesDel) are not applicable to this indel variant.
PP4 No patient phenotype or family history data is available for this case.
PP5 The variant is absent from ClinVar; no reputable source has reported this variant as pathogenic.
Benign
BA1 NM_004606.4:c.3811_3812delinsCC is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 The variant is absent from gnomAD, with an allele frequency of 0%.
BS2 The variant has not been observed in any individual in gnomAD, whether affected or healthy.
BS3 No in vitro or in vivo functional studies demonstrating no damaging effect on protein function or splicing are available for this variant.
BS4 No family segregation data is available.
BP1 BP1 applies to missense variants in genes for which primarily truncating variants are known to cause disease.
BP2 No observation in trans with a pathogenic variant has been reported.
BP3 BP3 applies to in-frame deletions/insertions in repetitive regions without known function.
BP4 SpliceAI predicts no splicing impact (max delta score 0.01), but REVEL and BayesDel scores are unavailable for this indel variant.
BP5 No data are available indicating this variant has been observed in a case with an alternate molecular basis for disease.
BP6 The variant is absent from ClinVar; no reputable source has classified this variant as benign.
BP7 BP7 applies to synonymous variants with no predicted splice impact.
N/A · 3 PM3 · PM4 · PM5
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. TAF1, a transcription factor, is infrequently altered in cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. COSMIC could not be reviewed because the browser session was redirected to the login page before search results were available.
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots