Is DVL1 p.Val669= (c.2007C>G) pathogenic?

DVL1 p.Val669= (c.2007C>G) is classified Likely benign in DVL1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-09-16). Very rare (popmax 0.00135%, afr).

How common is DVL1 p.Val669= (c.2007C>G) in the general population?

DVL1 p.Val669= (c.2007C>G) is very rare (popmax 0.00135%, afr) (gnomAD).

DVL1 p.Val669=

c.2007C>G · rs371155444 · VCV1629973

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00135%, afr)

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 -3.7	GERP -3.1
Overall
CADD	0.069	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00135% African / African-American · 1/74,230 alleles

Filtering AF 0.000297% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000215%

Overall 0.00064% 9/1,406,520 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00135%	74,230
European (non-Finnish)	0.000691%	144,693

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: DVL1
Protein: p.Val669=
Coding: c.2007C>G
MANE Select: NM_001330311
dbSNP: rs371155444
Type: single nucleotide variant
Location: chr1:1336223 (GRCh38)
Gene constraint: LOEUF 1.046 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.70 · 3 PDB

Full DVL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DVL1 p.Val669Asp Uncertain significance ★ ⚠ same residue
DVL1 p.Val669Ile Uncertain significance ★ ⚠ same residue
DVL1 p.Val669Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
DVL1 p.Ala125Val Uncertain significance ★★ ⚠ same type
DVL1 p.Ala288Val Uncertain significance ★★ ⚠ same type
DVL1 p.Ala361Thr Uncertain significance ★★ ⚠ same type
DVL1 p.Ala368Val Uncertain significance ★★ ⚠ same type
DVL1 p.Ala667Pro 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/dvl1-p-val669 (accessed [today's date]).

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