Is BAG6 p.Thr704= (c.2112C>T) pathogenic?

BAG6 p.Thr704= (c.2112C>T) is classified Likely benign in BAG6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-28). Ultra-rare (popmax 0.0259%, amr).

How common is BAG6 p.Thr704= (c.2112C>T) in the general population?

BAG6 p.Thr704= (c.2112C>T) is ultra-rare (popmax 0.0259%, amr) (gnomAD).

BAG6 p.Thr704=

c.2112C>T · VCV3985076

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0259%, amr)

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 -0.31	GERP -1.6
Overall
CADD	7.248	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0259% Admixed American · 13/50,146 alleles

Filtering AF 0.0153% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0121%

Overall 0.00387% 59/1,525,594 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0259%	3,857
Middle Eastern	0.0225%	4,444
Remaining individualsnot grpmax-eligible	0.0171%	5,852
Finnishnot grpmax-eligible	0.00732%	13,653
Ashkenazi Jewishnot grpmax-eligible	0.00359%	27,888
South Asian	0.00356%	28,083
European (non-Finnish)	0.00229%	43,594
African / African-American	0.00139%	71,720

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: BAG6
Protein: p.Thr704=
Coding: c.2112C>T
MANE Select: NM_001387994
Type: single nucleotide variant
Location: chr6:31642335 (GRCh38)
Gene constraint: LOEUF 0.265 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 58.52 · 10 PDB

Full BAG6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BAG6 p.Gln1137Glu Uncertain significance ★★ ⚠ same type
BAG6 p.Ala1101Val Uncertain significance ★ ⚠ same type
BAG6 p.Ala261Val Uncertain significance ★ ⚠ same type
BAG6 p.Arg1027Trp Uncertain significance ★ ⚠ same type
BAG6 p.Arg1099Trp Uncertain significance ★ ⚠ same type
BAG6 p.Arg1107Gln Uncertain significance ★ ⚠ same type
BAG6 p.Arg1133Gln Uncertain significance ★ ⚠ same type
BAG6 p.Arg1150Cys 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/bag6-p-thr704 (accessed [today's date]).

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