Is BPTF p.Arg1898= (c.5694G>A) pathogenic?

BPTF p.Arg1898= (c.5694G>A) is classified Benign/Likely benign in BPTF (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-27). Common (popmax 5.52%, afr) — too common for a highly-penetrant pathogenic allele; Associated with neurodevelopmental disorder with dysmorphic facies and distal limb anomalies.

BPTF p.Arg1898=

Q: What condition is associated with BPTF p.Arg1898= (c.5694G>A)?

BPTF p.Arg1898= (c.5694G>A) is associated with neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (ClinVar).

Q: How common is BPTF p.Arg1898= (c.5694G>A) in the general population?

BPTF p.Arg1898= (c.5694G>A) is common (popmax 5.52%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.5694G>A · rs59088743 · VCV785575

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 5.52%, afr) — too common for a highly-penetrant pathogenic allele

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.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.6	GERP 2, phastCons 1
Overall
CADD	9.712	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.52% African / African-American · 4,140/74,940 alleles

Filtering AF 5.38% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.33%

Overall 0.377% 6,085/1,613,652 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.52%	18
Middle Eastern	1.06%	95
Admixed American	0.908%	110
Remaining individualsnot grpmax-eligible	0.613%	163
Ashkenazi Jewishnot grpmax-eligible	0.314%	318
European (non-Finnish)	0.0714%	1,401
South Asian	0.0143%	6,998
Finnishnot grpmax-eligible	0.00781%	12,802
East Asian	0.00223%	44,884

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BPTF
Protein: p.Arg1898=
Coding: c.5694G>A
MANE Select: NM_182641
dbSNP: rs59088743
Type: single nucleotide variant
Location: chr17:67922976 (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.Arg1322Ter Pathogenic/Likely pathogenic ★★ same condition
BPTF p.Arg2858Ter Pathogenic ★★ same condition
BPTF p.Arg2058Cys Uncertain significance ★★ same condition
BPTF p.Arg2139His Uncertain significance ★★ ⚠ same condition
BPTF p.Arg2858Gln Uncertain significance ★★ ⚠ same condition
BPTF p.Arg542Gln Uncertain significance ★★ same condition
BPTF p.Arg68Ser Uncertain significance ★★ ⚠ same condition
BPTF p.Asn452Ser Uncertain significance ★★ ⚠ 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-arg1898 (accessed [today's date]).

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