Is DSPP p.Ser980Arg (c.2940C>G) pathogenic?

DSPP p.Ser980Arg (c.2940C>G) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-19). AlphaMissense: likely pathogenic (0.7823); Very rare (popmax 0.00197%, amr); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Ser980Arg (c.2940C>G)?

DSPP p.Ser980Arg (c.2940C>G) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Ser980Arg (c.2940C>G) in the general population?

DSPP p.Ser980Arg (c.2940C>G) is very rare (popmax 0.00197%, amr) (gnomAD).

What do computational predictors say about DSPP p.Ser980Arg (c.2940C>G)?

AlphaMissense predicts likely pathogenic (score 0.7823) — an in-silico prediction, not a clinical call.

DSPP p.Ser980Arg

c.2940C>G · VCV3505572

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7823 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00197%, amr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.7823	likely pathogenic
REVEL	0.15	moderately benign-leaning
SaProt	LLR -12.31	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 -7.1	GERP -1.4
Regional constraint	o/e 0.73	unconstrained · MANE · 1,389 bp · p 1.3e-11 · regional, not allelic
Overall
CADD	0.028	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 0.00197% Admixed American · 1/50,674 alleles

Filtering AF 2.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000323% 5/1,546,692 alleles · very rare exomes 3/1,398,348 · genomes 2/148,344 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00197%	50,674
Remaining individualsnot grpmax-eligible	0.00167%	59,990
African / African-American	0.00143%	69,808
European (non-Finnish)	0.000174%	573,207

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.Ser980Arg
Coding: c.2940C>G
MANE Select: NM_014208
Type: single nucleotide variant
Location: chr4:87615602 (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-ser980arg (accessed [today's date]).

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