Is DSPP p.Ser1079Cys (c.3235A>T) pathogenic?

DSPP p.Ser1079Cys (c.3235A>T) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-02). AlphaMissense: ambiguous (0.5255); No allele count reported in gnomAD v4.1 (AN 1,445,692); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Ser1079Cys (c.3235A>T)?

DSPP p.Ser1079Cys (c.3235A>T) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Ser1079Cys (c.3235A>T) in the general population?

DSPP p.Ser1079Cys (c.3235A>T) is no allele count reported in gnomAD v4.1 (AN 1,445,692) (gnomAD).

What do computational predictors say about DSPP p.Ser1079Cys (c.3235A>T)?

AlphaMissense predicts ambiguous (score 0.5255) — an in-silico prediction, not a clinical call.

DSPP p.Ser1079Cys

c.3235A>T · rs2475886473 · VCV3086004

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5255 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,445,692)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.5255	ambiguous
REVEL	0.177	moderately benign-leaning
SaProt	LLR -13.33	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.1	GERP 0.88, phastCons 0.017
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	16.97	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 1,445,692). 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.Ser1079Cys
Coding: c.3235A>T
dbSNP: rs2475886473
Type: single nucleotide variant
Location: chr4:87615897 (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-ser1079cys (accessed [today's date]).

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