Is DSPP p.Asp1236= (c.3708C>T) pathogenic?

DSPP p.Asp1236= (c.3708C>T) is classified Benign/Likely benign in DSPP (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-02-16). Common (popmax 14.5%, afr) — too common for a highly-penetrant pathogenic allele.

DSPP p.Asp1236=

Q: How common is DSPP p.Asp1236= (c.3708C>T) in the general population?

DSPP p.Asp1236= (c.3708C>T) is common (popmax 14.5%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.3708C>T · rs111884410 · VCV811552

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 14.5%, afr) — too common for a highly-penetrant pathogenic allele

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 -5.2	GERP -3.4
Overall
CADD	0.573	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 14.5% African / African-American · 7,029/48,396 alleles

Filtering AF 14.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 14.1%

Overall 1.85% 25,919/1,402,724 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	14.5%	7
Finnishnot grpmax-eligible	5.29%	19
Ashkenazi Jewishnot grpmax-eligible	3.19%	31
Middle Eastern	2.96%	34
Remaining individualsnot grpmax-eligible	2.68%	37
Admixed American	1.98%	50
South Asian	1.81%	55
European (non-Finnish)	1.05%	95
East Asian	0.518%	193

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.Asp1236=
Coding: c.3708C>T
dbSNP: rs111884410
Type: single nucleotide variant
Location: chr4:87616370 (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-asp1236 (accessed [today's date]).

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