Is ADPRS p.Asp96= (c.288C>T) pathogenic?

ADPRS p.Asp96= (c.288C>T) is classified Likely benign in ADPRS (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-01). Rare (popmax 0.132%, mid).

How common is ADPRS p.Asp96= (c.288C>T) in the general population?

ADPRS p.Asp96= (c.288C>T) is rare (popmax 0.132%, mid) (gnomAD).

ADPRS p.Asp96=

c.288C>T · rs139465196 · VCV2638666

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.132%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.7	GERP -3.6
Overall
CADD	11.51	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.132% Middle Eastern · 8/6,062 alleles

Filtering AF 0.0953% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0888%

Overall 0.0165% 267/1,614,134 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.135%	740
Middle Easterngrpmax	0.132%	758
South Asian	0.113%	884
Remaining individualsnot grpmax-eligible	0.0368%	2,718
Admixed American	0.00833%	12,003
European (non-Finnish)	0.00712%	14,048
African / African-American	0.004%	25,015
East Asian	0.00223%	44,888

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ADPRS
Protein: p.Asp96=
Coding: c.288C>T
MANE Select: NM_017825
dbSNP: rs139465196
Type: single nucleotide variant
Location: chr1:36091320 (GRCh38)
Gene constraint: LOEUF 1.155 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.70 · 14 PDB

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

Similar variants

ADPRS p.Gln106Ter Pathogenic/Likely pathogenic ★★ same type
ADPRS p.Ser177Leu Likely pathogenic ★★ same type
ADPRS p.Thr79Pro Pathogenic/Likely pathogenic ★★ same type
ADPRS p.Val335Gly Pathogenic/Likely pathogenic ★★ same type
ADPRS p.Ala94Asp Uncertain significance ★★ ⚠ same type
ADPRS p.Arg175Trp Uncertain significance ★★ ⚠ same type
ADPRS p.Pro336Leu Uncertain significance ★★ ⚠ same type
ADPRS p.Tyr164Cys Uncertain significance ★★ ⚠ same type

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/adprs-p-asp96 (accessed [today's date]).

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