Is DSPP p.Ser1160= (c.3480T>C) pathogenic?

DSPP p.Ser1160= (c.3480T>C) is classified Likely benign in DSPP (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-01). Rare (popmax 0.973%, mid); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Ser1160= (c.3480T>C)?

DSPP p.Ser1160= (c.3480T>C) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Ser1160= (c.3480T>C) in the general population?

DSPP p.Ser1160= (c.3480T>C) is rare (popmax 0.973%, mid) (gnomAD).

DSPP p.Ser1160=

c.3480T>C · rs111216206 · VCV2654921

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.973%, mid)

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
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -1.7
Overall
CADD	1.266	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.973% Middle Eastern · 49/5,034 alleles

Filtering AF 0.756% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.679%

Overall 0.0725% 1,064/1,468,504 alleles · rare exomes 952/1,348,194 · genomes 112/120,310 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.973%	103
South Asian	0.236%	423
Ashkenazi Jewishnot grpmax-eligible	0.185%	540
Remaining individualsnot grpmax-eligible	0.122%	819
Admixed American	0.0887%	1,127
European (non-Finnish)	0.0585%	1,708
Finnishnot grpmax-eligible	0.0228%	4,378
African / African-American	0.0185%	5,399
East Asian	0.00515%	19,400

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.Ser1160=
Coding: c.3480T>C
MANE Select: NM_014208
dbSNP: rs111216206
Type: single nucleotide variant
Location: chr4:87616142 (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-ser1160 (accessed [today's date]).

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