Is DSPP p.Tyr6Asp (c.16T>G) pathogenic?

DSPP p.Tyr6Asp (c.16T>G) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 2 submitters; last evaluated 2025-04-22). AlphaMissense: likely pathogenic (0.9075); Absent from gnomAD v4.1; Associated with Pulp calcification.

What condition is associated with DSPP p.Tyr6Asp (c.16T>G)?

DSPP p.Tyr6Asp (c.16T>G) is associated with Pulp calcification (ClinVar).

How common is DSPP p.Tyr6Asp (c.16T>G) in the general population?

DSPP p.Tyr6Asp (c.16T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DSPP p.Tyr6Asp (c.16T>G)?

AlphaMissense predicts likely pathogenic (score 0.9075) — an in-silico prediction, not a clinical call.

DSPP p.Tyr6Asp

c.16T>G · rs121912988 · VCV16857

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9075 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Pulp calcification

Computational evidence

Protein change
AlphaMissense	0.9075	likely pathogenic
REVEL	0.63	indeterminate
SaProt	LLR -12.07	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.1	GERP 1.8, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 3,360 bp · p 0.63 · regional, not allelic
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DSPP
Protein: p.Tyr6Asp
Coding: c.16T>G
MANE Select: NM_014208
dbSNP: rs121912988
Type: single nucleotide variant
Location: chr4:87610924 (GRCh38)

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

Disease context

Pulp calcification — 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-tyr6asp (accessed [today's date]).

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