Is DSPP p.Ser1204= (c.3612T>C) pathogenic?

DSPP p.Ser1204= (c.3612T>C) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-05). Low-frequency (popmax 2.64%, afr); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Ser1204= (c.3612T>C)?

DSPP p.Ser1204= (c.3612T>C) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Ser1204= (c.3612T>C) in the general population?

DSPP p.Ser1204= (c.3612T>C) is low-frequency (popmax 2.64%, afr) (gnomAD).

DSPP p.Ser1204=

c.3612T>C · rs371154871 · VCV3086025

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 2.64%, afr)

Conditions

Inborn genetic diseases

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 -12	GERP -3.2
Overall
CADD	1.036	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.64% African / African-American · 796/30,116 alleles

Filtering AF 2.49% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.43%

Overall 0.351% 3,938/1,121,124 alleles · low-frequency

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	17.2%	6
African / African-Americangrpmax	2.64%	38
Admixed American	1.64%	61
Ashkenazi Jewishnot grpmax-eligible	0.523%	191
Finnishnot grpmax-eligible	0.458%	218
East Asian	0.384%	261
South Asian	0.291%	343
Remaining individualsnot grpmax-eligible	0.28%	357
Middle Eastern	0.243%	411
European (non-Finnish)	0.229%	436

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ser1204=
Coding: c.3612T>C
dbSNP: rs371154871
Type: single nucleotide variant
Location: chr4:87616274 (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-ser1204 (accessed [today's date]).

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