Is DSPP p.Asp1167= (c.3501C>T) pathogenic?

DSPP p.Asp1167= (c.3501C>T) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-08). Rare (popmax 0.455%, afr); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Asp1167= (c.3501C>T)?

DSPP p.Asp1167= (c.3501C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Asp1167= (c.3501C>T) in the general population?

DSPP p.Asp1167= (c.3501C>T) is rare (popmax 0.455%, afr) (gnomAD).

DSPP p.Asp1167=

c.3501C>T · VCV3505582

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.455%, afr)

Conditions

Inborn genetic diseases

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 -8.3	GERP -1.7
Overall
CADD	0.027	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.455% African / African-American · 282/61,986 alleles

Filtering AF 0.411% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.394%

Overall 0.0239% 366/1,528,398 alleles · rare exomes 260/1,385,994 · genomes 106/142,404 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.455%	220
Remaining individualsnot grpmax-eligible	0.061%	1,639
Admixed American	0.0584%	1,713
South Asian	0.00362%	27,636
European (non-Finnish)	0.0014%	71,276

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.Asp1167=
Coding: c.3501C>T
MANE Select: NM_014208
Type: single nucleotide variant
Location: chr4:87616163 (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-asp1167 (accessed [today's date]).

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