Is DACH1 p.Gln660Arg (c.1979A>G) pathogenic?

DACH1 p.Gln660Arg (c.1979A>G) is classified Uncertain significance in DACH1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-19). AlphaMissense: likely benign (0.3111); Very rare (popmax 0.00907%, nfe).

How common is DACH1 p.Gln660Arg (c.1979A>G) in the general population?

DACH1 p.Gln660Arg (c.1979A>G) is very rare (popmax 0.00907%, nfe) (gnomAD).

What do computational predictors say about DACH1 p.Gln660Arg (c.1979A>G)?

AlphaMissense predicts likely benign (score 0.3111) — an in-silico prediction, not a clinical call.

DACH1 p.Gln660Arg

c.1979A>G · VCV4658356

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3111 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00907%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3111	likely benign
REVEL	0.182	moderately benign-leaning
SaProt	LLR -7.25	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.6, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 425 kb · p 0.0017 · regional, not allelic
Overall
CADD	27.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM Q712R vs ClinVar Q660R) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00907% European (non-Finnish) · 107/1,179,874 alleles

Filtering AF 0.00766% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00708%

Overall 0.00688% 111/1,613,370 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00907%	11,027
Remaining individualsnot grpmax-eligible	0.0032%	31,227
Admixed American	0.00167%	59,830
African / African-American	0.00134%	74,886

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: DACH1
Protein: p.Gln660Arg
Coding: c.1979A>G
MANE Select: NM_080759
Type: single nucleotide variant
Location: chr13:71475741 (GRCh38)
Gene constraint: LOEUF 0.371 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 58.74 · 1 PDB
Residue 660: the 'interaction with sin3a' region; the 'dachbox-c' region

Full DACH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DACH1 p.Val375= Benign ★★ same type
DACH1 c.1722+6C>T Conflicting classifications of pathogenicity ★ same type
DACH1 p.Ala109Val Uncertain significance ★ ⚠ same type
DACH1 p.Ala36Glu Uncertain significance ★ ⚠ same type
DACH1 p.Ala36Val Uncertain significance ★ ⚠ same type
DACH1 p.Ala418Thr Uncertain significance ★ ⚠ same type
DACH1 p.Ala533Thr Uncertain significance ★ ⚠ same type
DACH1 p.Ala586Thr 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/dach1-p-gln660arg (accessed [today's date]).

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