Is DOLPP1 p.Ser153Gly (c.457A>G) pathogenic?

DOLPP1 p.Ser153Gly (c.457A>G) is classified Uncertain significance in DOLPP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-21). AlphaMissense: likely benign (0.1892); Absent from gnomAD v4.1.

How common is DOLPP1 p.Ser153Gly (c.457A>G) in the general population?

DOLPP1 p.Ser153Gly (c.457A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DOLPP1 p.Ser153Gly (c.457A>G)?

AlphaMissense predicts likely benign (score 0.1892) — an in-silico prediction, not a clinical call.

DOLPP1 p.Ser153Gly

c.457A>G · VCV3842099

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1892 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1892	likely benign
REVEL	0.812	moderately pathogenic-leaning
SaProt	LLR -10.30	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 7,872 bp · p 0.00091 · regional, not allelic
Overall
CADD	23.6	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DOLPP1
Protein: p.Ser153Gly
Coding: c.457A>G
MANE Select: NM_020438
Type: single nucleotide variant
Location: chr9:129085612 (GRCh38)
Gene constraint: LOEUF 0.69 · pLI 0.08 (gnomAD)
Structure: AlphaFold pLDDT 89.92

Full DOLPP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DOLPP1 p.Ala224Val Uncertain significance ★ ⚠ same type
DOLPP1 p.Arg206Gln Uncertain significance ★ ⚠ same type
DOLPP1 p.Arg229Gly Uncertain significance ★ ⚠ same type
DOLPP1 p.Asn213Ser Uncertain significance ★ ⚠ same type
DOLPP1 p.Asn78Thr Uncertain significance ★ ⚠ same type
DOLPP1 p.Gln6Glu Uncertain significance ★ ⚠ same type
DOLPP1 p.Gly65Asp Uncertain significance ★ ⚠ same type
DOLPP1 p.His31Tyr 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/dolpp1-p-ser153gly (accessed [today's date]).

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