Is PLD1 p.Ala802Asp (c.2405C>A) pathogenic?

PLD1 p.Ala802Asp (c.2405C>A) is classified Uncertain significance in PLD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-19). AlphaMissense: likely pathogenic (0.8906); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with PLD1 p.Ala802Asp (c.2405C>A)?

PLD1 p.Ala802Asp (c.2405C>A) is associated with Inborn genetic diseases (ClinVar).

How common is PLD1 p.Ala802Asp (c.2405C>A) in the general population?

PLD1 p.Ala802Asp (c.2405C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PLD1 p.Ala802Asp (c.2405C>A)?

AlphaMissense predicts likely pathogenic (score 0.8906) — an in-silico prediction, not a clinical call.

PLD1 p.Ala802Asp

c.2405C>A · VCV3933868

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8906 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,788)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8906	likely pathogenic
REVEL	0.737	pathogenic-leaning
SaProt	LLR -13.12	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.6	GERP 0.098, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 135 kb · p 0.57 · regional, not allelic
Overall
CADD	26.5	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

No allele count reported in gnomAD v4.1 (AN 1,612,788). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PLD1
Protein: p.Ala802Asp
Coding: c.2405C>A
MANE Select: NM_002662
Type: single nucleotide variant
Location: chr3:171659237 (GRCh38)
Gene constraint: LOEUF 0.822 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.92 · 2 PDB
Residue 802: an α-helix; the 'catalytic' region

Full PLD1 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

Similar variants

PLD1 p.Ala689Val Uncertain significance ★★ ⚠ same condition
PLD1 p.Ala765Thr Uncertain significance ★★ ⚠ same condition
PLD1 p.Arg172Lys Uncertain significance ★★ ⚠ same condition
PLD1 p.Arg317Trp Uncertain significance ★★ ⚠ same condition
PLD1 p.Arg917His Uncertain significance ★★ ⚠ same condition
PLD1 p.Asn905Lys Uncertain significance ★★ ⚠ same condition
PLD1 p.Asp1018Asn Uncertain significance ★★ ⚠ same condition
PLD1 p.Asp799Asn Uncertain significance ★★ ⚠ same condition

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/pld1-p-ala802asp (accessed [today's date]).

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