Is DSPP p.Asp1164= (c.3492T>C) pathogenic?

DSPP p.Asp1164= (c.3492T>C) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-30). Low-frequency (popmax 1.25%, amr); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Asp1164= (c.3492T>C)?

DSPP p.Asp1164= (c.3492T>C) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Asp1164= (c.3492T>C) in the general population?

DSPP p.Asp1164= (c.3492T>C) is low-frequency (popmax 1.25%, amr) (gnomAD).

DSPP p.Asp1164=

c.3492T>C · rs374381786 · VCV3086021

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.25%, amr)

Conditions

Inborn genetic diseases

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 -20	GERP -2.3
Overall
CADD	0.42	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.25% Admixed American · 224/17,970 alleles

Filtering AF 1.11% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.06%

Overall 0.305% 2,241/735,932 alleles · low-frequency

Ancestry group	Frequency	1 in
Admixed Americangrpmax	1.25%	80
Amishnot grpmax-eligible	0.893%	112
Finnishnot grpmax-eligible	0.768%	130
Middle Eastern	0.606%	165
Ashkenazi Jewishnot grpmax-eligible	0.556%	180
South Asian	0.544%	184
African / African-American	0.408%	245
Remaining individualsnot grpmax-eligible	0.394%	254
East Asian	0.373%	268
European (non-Finnish)	0.218%	459

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.Asp1164=
Coding: c.3492T>C
dbSNP: rs374381786
Type: single nucleotide variant
Location: chr4:87616154 (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-asp1164 (accessed [today's date]).

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