Is DUT p.Val109= (c.327G>A) pathogenic?

DUT p.Val109= (c.327G>A) is classified Likely benign in DUT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-01). Ultra-rare (popmax 0.0165%, mid).

How common is DUT p.Val109= (c.327G>A) in the general population?

DUT p.Val109= (c.327G>A) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

DUT p.Val109=

c.327G>A · rs780081759 · VCV2645309

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

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 0.006	GERP -1.5
Overall
CADD	5.115	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,052 alleles

Filtering AF 0.0075% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00701%

Overall 0.00758% 122/1,608,864 alleles · ultra-rare exomes 114/1,456,672 · genomes 8/152,192 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,052
Ashkenazi Jewishnot grpmax-eligible	0.0102%	9,807
European (non-Finnish)	0.00891%	11,223
South Asian	0.00771%	12,975
Remaining individualsnot grpmax-eligible	0.00642%	15,568
African / African-American	0.00269%	37,167

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: DUT
Protein: p.Val109=
Coding: c.327G>A
MANE Select: NM_001025248
dbSNP: rs780081759
Type: single nucleotide variant
Location: chr15:48332314 (GRCh38)
Gene constraint: LOEUF 1.684 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.51 · 12 PDB

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

Similar variants

DUT p.Tyr142Cys Likely pathogenic ★ ⚠ same type
DUT p.Ala235Ser Uncertain significance ★ ⚠ same type
DUT p.Arg173Trp Uncertain significance ★ ⚠ same type
DUT p.Arg216Gln Uncertain significance ★ ⚠ same type
DUT p.Asp192His Uncertain significance ★ ⚠ same type
DUT p.Gln219His Uncertain significance ★ ⚠ same type
DUT p.Glu223Lys Uncertain significance ★ ⚠ same type
DUT p.Glu240Lys 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/dut-p-val109 (accessed [today's date]).

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