Is DSPP p.Ser1082Asn (c.3245G>A) pathogenic?

DSPP p.Ser1082Asn (c.3245G>A) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-23). AlphaMissense: likely benign (0.2828); Very rare (popmax 0.00619%, eas); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Ser1082Asn (c.3245G>A)?

DSPP p.Ser1082Asn (c.3245G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Ser1082Asn (c.3245G>A) in the general population?

DSPP p.Ser1082Asn (c.3245G>A) is very rare (popmax 0.00619%, eas) (gnomAD).

What do computational predictors say about DSPP p.Ser1082Asn (c.3245G>A)?

AlphaMissense predicts likely benign (score 0.2828) — an in-silico prediction, not a clinical call.

DSPP p.Ser1082Asn

c.3245G>A · rs1273546928 · VCV2603246

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2828 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00619%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2828	likely benign
REVEL	0.107	moderately benign-leaning
SaProt	LLR -8.93	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.85	GERP 0.15
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	9.757	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00619% East Asian · 2/32,316 alleles

Filtering AF 0.00103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000383%

Overall 0.00142% 16/1,125,140 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00619%	16,158
Finnishnot grpmax-eligible	0.00418%	23,928
Admixed American	0.00318%	31,486
South Asian	0.00291%	34,400
Remaining individualsnot grpmax-eligible	0.00209%	47,824
European (non-Finnish)	0.000961%	104,029

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.Ser1082Asn
Coding: c.3245G>A
dbSNP: rs1273546928
Type: single nucleotide variant
Location: chr4:87615907 (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-ser1082asn (accessed [today's date]).

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