Is BTBD9 p.Val239= (c.717G>A) pathogenic?

BTBD9 p.Val239= (c.717G>A) is classified Benign in BTBD9 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Rare (popmax 0.502%, nfe).

How common is BTBD9 p.Val239= (c.717G>A) in the general population?

BTBD9 p.Val239= (c.717G>A) is rare (popmax 0.502%, nfe) (gnomAD).

BTBD9 p.Val239=

c.717G>A · rs41303370 · VCV787827

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.502%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.48 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.56	GERP -1.2, phastCons 1
Overall
CADD	8.599	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.502% European (non-Finnish) · 5,924/1,180,026 alleles

Filtering AF 0.491% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.487%

Overall 0.429% 6,931/1,614,114 alleles · rare exomes 6,461/1,461,892 · genomes 470/152,222 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.74%	135
European (non-Finnish)grpmax	0.502%	199
Remaining individualsnot grpmax-eligible	0.397%	252
Admixed American	0.177%	566
Middle Eastern	0.132%	758
South Asian	0.114%	876
African / African-American	0.0867%	1,154
East Asian	0.00446%	22,436

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: BTBD9
Protein: p.Val239=
Coding: c.717G>A
MANE Select: NM_001099272
dbSNP: rs41303370
Type: single nucleotide variant
Location: chr6:38592673 (GRCh38)
Gene constraint: LOEUF 0.959 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.71
Residue 239: the back domain

Full BTBD9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BTBD9 p.Ala100Val Uncertain significance ★ ⚠ same type
BTBD9 p.Ala28Thr Uncertain significance ★ ⚠ same type
BTBD9 p.Ala476Thr Uncertain significance ★ ⚠ same type
BTBD9 p.Ala590Val Uncertain significance ★ ⚠ same type
BTBD9 p.Ala76Val Uncertain significance ★ ⚠ same type
BTBD9 p.Arg257Gly Uncertain significance ★ ⚠ same type
BTBD9 p.Arg319His Uncertain significance ★ ⚠ same type
BTBD9 p.Arg336Gly Uncertain significance ★ ⚠ same type

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/btbd9-p-val239 (accessed [today's date]).

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