Is DPH1 p.Ala282Ser (c.844G>T) pathogenic?

DPH1 p.Ala282Ser (c.844G>T) is classified Likely benign in DPH1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-09-25). AlphaMissense: likely benign (0.1007); Rare (popmax 0.134%, eas).

How common is DPH1 p.Ala282Ser (c.844G>T) in the general population?

DPH1 p.Ala282Ser (c.844G>T) is rare (popmax 0.134%, eas) (gnomAD).

What do computational predictors say about DPH1 p.Ala282Ser (c.844G>T)?

AlphaMissense predicts likely benign (score 0.1007) — an in-silico prediction, not a clinical call.

DPH1 p.Ala282Ser

c.844G>T · rs199982638 · VCV726451

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1007 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.134%, eas)

Computational evidence

Protein change
AlphaMissense	0.1007	likely benign
REVEL	0.313	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 12 kb · p 0.074 · regional, not allelic
Overall
CADD	23.1	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM A287S vs ClinVar A282S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.134% East Asian · 60/44,886 alleles

Filtering AF 0.107% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0968%

Overall 0.00409% 66/1,614,102 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.134%	748
Remaining individualsnot grpmax-eligible	0.0096%	10,418

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: DPH1
Protein: p.Ala282Ser
Coding: c.844G>T
MANE Select: NM_001383
dbSNP: rs199982638
Type: single nucleotide variant
Location: chr17:2040312 (GRCh38)
Gene constraint: LOEUF 1.321 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.00

Full DPH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPH1 p.Leu229Pro Pathogenic/Likely pathogenic ★★ same type
DPH1 p.Arg144Trp Uncertain significance ★★ ⚠ same type
DPH1 p.Arg22Gln Uncertain significance ★★ ⚠ same type
DPH1 p.Arg27His Uncertain significance ★★ ⚠ same type
DPH1 p.Arg47Trp Uncertain significance ★★ ⚠ same type
DPH1 p.Asp231Glu Uncertain significance ★★ ⚠ same type
DPH1 p.Gln269His Uncertain significance ★★ ⚠ same type
DPH1 p.Ile241Phe 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/dph1-p-ala282ser (accessed [today's date]).

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