Is DSPP p.Ser1139Gly (c.3415A>G) pathogenic?

DSPP p.Ser1139Gly (c.3415A>G) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-27). AlphaMissense: likely benign (0.2208); No allele count reported in gnomAD v4.1 (AN 1,124,670); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Ser1139Gly (c.3415A>G)?

DSPP p.Ser1139Gly (c.3415A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Ser1139Gly (c.3415A>G) in the general population?

DSPP p.Ser1139Gly (c.3415A>G) is no allele count reported in gnomAD v4.1 (AN 1,124,670) (gnomAD).

What do computational predictors say about DSPP p.Ser1139Gly (c.3415A>G)?

AlphaMissense predicts likely benign (score 0.2208) — an in-silico prediction, not a clinical call.

DSPP p.Ser1139Gly

c.3415A>G · rs2475887016 · VCV2286337

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2208 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,124,670)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2208	likely benign
REVEL	0.179	moderately benign-leaning
SaProt	LLR -12.16	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 0.86	GERP -0.23
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	19.12	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

No allele count reported in gnomAD v4.1 (AN 1,124,670). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DSPP
Protein: p.Ser1139Gly
Coding: c.3415A>G
dbSNP: rs2475887016
Type: single nucleotide variant
Location: chr4:87616077 (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-ser1139gly (accessed [today's date]).

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