Is BPTF p.Pro1855fs (c.5564del) pathogenic?

BPTF p.Pro1855fs (c.5564del) is classified Likely pathogenic in BPTF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-05-27). Absent from gnomAD; Associated with neurodevelopmental disorder with dysmorphic facies and distal limb anomalies.

What condition is associated with BPTF p.Pro1855fs (c.5564del)?

BPTF p.Pro1855fs (c.5564del) is associated with neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (ClinVar).

How common is BPTF p.Pro1855fs (c.5564del) in the general population?

BPTF p.Pro1855fs (c.5564del) is absent from gnomAD (gnomAD).

BPTF p.Pro1855fs

c.5564del · rs2147246788 · VCV1341680

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder with dysmorphic facies and distal limb anomalies

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 14 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.48	GERP -1.5, phastCons 0.8
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BPTF
Protein: p.Pro1855fs
Coding: c.5564del
MANE Select: NM_182641
dbSNP: rs2147246788
Type: Deletion
Location: chr17:67922845 (GRCh38)
Gene constraint: LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

Full BPTF gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder with dysmorphic facies and distal limb anomalies — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BPTF p.Arg2854fs Likely pathogenic ★ same condition
BPTF p.Asp2751fs Likely pathogenic ★ same condition
BPTF p.Gly94fs Likely pathogenic ★ same condition
BPTF p.His1985fs Likely pathogenic ★ same condition
BPTF p.Leu330fs Pathogenic ★ same condition
BPTF p.Lys1053fs Pathogenic ★ same condition
BPTF p.Thr1819fs Likely pathogenic ★ same condition
BPTF p.Val2188fs Pathogenic ★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bptf-p-pro1855fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown