Is DSPP p.Ser1067Gly (c.3199A>G) pathogenic?

DSPP p.Ser1067Gly (c.3199A>G) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-30). AlphaMissense: likely benign (0.2465); Very rare (popmax 8.73e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Ser1067Gly (c.3199A>G)?

DSPP p.Ser1067Gly (c.3199A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Ser1067Gly (c.3199A>G) in the general population?

DSPP p.Ser1067Gly (c.3199A>G) is very rare (popmax 8.73e-05%, nfe) (gnomAD).

What do computational predictors say about DSPP p.Ser1067Gly (c.3199A>G)?

AlphaMissense predicts likely benign (score 0.2465) — an in-silico prediction, not a clinical call.

DSPP p.Ser1067Gly

c.3199A>G · rs1727897154 · VCV2322696

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2465 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.73e-05%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2465	likely benign
REVEL	0.165	moderately benign-leaning
SaProt	LLR -11.77	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.66	GERP -0.19
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	18.23	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

Grpmax group 8.73e-05% European (non-Finnish) · 1/1,144,820 alleles

Overall 7.17e-05% 1/1,395,528 alleles · very rare

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: DSPP
Protein: p.Ser1067Gly
Coding: c.3199A>G
dbSNP: rs1727897154
Type: single nucleotide variant
Location: chr4:87615861 (GRCh38)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/dspp-p-ser1067gly (accessed [today's date]).

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