Is DSPP p.Ser792Gly (c.2374A>G) pathogenic?

DSPP p.Ser792Gly (c.2374A>G) is classified Likely benign in DSPP (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-14). AlphaMissense: likely benign (0.1665); Low-frequency (popmax 1.09%, afr).

How common is DSPP p.Ser792Gly (c.2374A>G) in the general population?

DSPP p.Ser792Gly (c.2374A>G) is low-frequency (popmax 1.09%, afr) (gnomAD).

What do computational predictors say about DSPP p.Ser792Gly (c.2374A>G)?

AlphaMissense predicts likely benign (score 0.1665) — an in-silico prediction, not a clinical call.

DSPP p.Ser792Gly

c.2374A>G · rs201148490 · VCV1200988

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1665 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.09%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1665	likely benign
REVEL	0.13	moderately benign-leaning
SaProt	LLR -11.77	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.4	GERP 0.73, phastCons 0.27
Regional constraint	o/e 0.73	unconstrained · MANE · 1,389 bp · p 1.3e-11 · regional, not allelic
Overall
CADD	3.772	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 1.09% African / African-American · 795/73,024 alleles

Filtering AF 1.03% ClinGen BA1/BS1 input FAF95, joint · FAF99 1%

Overall 0.0585% 908/1,551,228 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.09%	92
Remaining individualsnot grpmax-eligible	0.0899%	1,113
Admixed American	0.0863%	1,158
Middle Eastern	0.0669%	1,495
South Asian	0.00833%	12,008
European (non-Finnish)	0.000349%	286,696

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.Ser792Gly
Coding: c.2374A>G
dbSNP: rs201148490
Type: single nucleotide variant
Location: chr4:87615036 (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-ser792gly (accessed [today's date]).

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