Is DSPP p.Ser1079Arg (c.3237T>G) pathogenic?

DSPP p.Ser1079Arg (c.3237T>G) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-12). AlphaMissense: likely pathogenic (0.6538); Rare (popmax 0.195%, eas); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Ser1079Arg (c.3237T>G)?

DSPP p.Ser1079Arg (c.3237T>G) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Ser1079Arg (c.3237T>G) in the general population?

DSPP p.Ser1079Arg (c.3237T>G) is rare (popmax 0.195%, eas) (gnomAD).

What do computational predictors say about DSPP p.Ser1079Arg (c.3237T>G)?

AlphaMissense predicts likely pathogenic (score 0.6538) — an in-silico prediction, not a clinical call.

DSPP p.Ser1079Arg

c.3237T>G · rs371970214 · VCV2279202

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6538 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.195%, eas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6538	likely pathogenic
REVEL	0.219	benign-leaning
SaProt	LLR -11.93	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -2
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	0.517	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 0.195% East Asian · 70/35,966 alleles

Filtering AF 0.158% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.145%

Overall 0.0355% 490/1,378,560 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.195%	514
Finnishnot grpmax-eligible	0.131%	766
Remaining individualsnot grpmax-eligible	0.0489%	2,045
Admixed American	0.0282%	3,540
European (non-Finnish)	0.0264%	3,790
Ashkenazi Jewishnot grpmax-eligible	0.0263%	3,796
Middle Eastern	0.0196%	5,114
South Asian	0.0164%	6,087
African / African-American	0.00992%	10,079

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.Ser1079Arg
Coding: c.3237T>G
dbSNP: rs371970214
Type: single nucleotide variant
Location: chr4:87615899 (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-ser1079arg (accessed [today's date]).

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