Is DSPP p.Gly168= (c.504C>T) pathogenic?

DSPP p.Gly168= (c.504C>T) is classified Likely benign in DSPP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-12-02). Very rare (popmax 0.00879%, sas).

How common is DSPP p.Gly168= (c.504C>T) in the general population?

DSPP p.Gly168= (c.504C>T) is very rare (popmax 0.00879%, sas) (gnomAD).

DSPP p.Gly168=

c.504C>T · rs539814032 · VCV1370654

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00879%, sas)

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 -0.023	GERP -3.7
Overall
CADD	1.786	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00879% South Asian · 8/91,062 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.00211% 34/1,614,022 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00879%	11,383
African / African-American	0.00667%	15,001
Remaining individualsnot grpmax-eligible	0.0048%	20,837
Admixed American	0.00333%	29,999
European (non-Finnish)	0.00136%	73,749

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.Gly168=
Coding: c.504C>T
dbSNP: rs539814032
Type: single nucleotide variant
Location: chr4:87612690 (GRCh38)

Full DSPP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-gly168 (accessed [today's date]).

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