Is DVL1 p.Ala234= (c.702C>T) pathogenic?

DVL1 p.Ala234= (c.702C>T) is classified Benign/Likely benign in DVL1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-12). Rare (popmax 0.131%, afr).

How common is DVL1 p.Ala234= (c.702C>T) in the general population?

DVL1 p.Ala234= (c.702C>T) is rare (popmax 0.131%, afr) (gnomAD).

DVL1 p.Ala234=

c.702C>T · rs141536842 · VCV1556553

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.131%, 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 -0.072	GERP -5.3, phastCons 0.18
Overall
CADD	5.798	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.131% African / African-American · 98/75,028 alleles

Filtering AF 0.11% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.102%

Overall 0.00805% 130/1,613,952 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.131%	766
Admixed American	0.02%	5,002
Remaining individualsnot grpmax-eligible	0.0112%	8,929
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,867
East Asian	0.00223%	44,874
European (non-Finnish)	0.000763%	131,110

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.Ala234=
Coding: c.702C>T
MANE Select: NM_001330311
dbSNP: rs141536842
Type: single nucleotide variant
Location: chr1:1340314 (GRCh38)
Gene constraint: LOEUF 1.046 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.70 · 3 PDB
Residue 234: the 'disordered' region

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

Similar variants

DVL1 p.Ala234Val 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
DVL1 p.Arg108Trp Uncertain significance ★★ ⚠ same type
DVL1 p.Arg116Gln 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-ala234 (accessed [today's date]).

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