Is PLD1 p.Val1024Ile (c.3070G>A) pathogenic?

PLD1 p.Val1024Ile (c.3070G>A) is classified Benign/Likely benign in PLD1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-26). AlphaMissense: likely benign (0.0569); Low-frequency (popmax 2.07%, afr).

How common is PLD1 p.Val1024Ile (c.3070G>A) in the general population?

PLD1 p.Val1024Ile (c.3070G>A) is low-frequency (popmax 2.07%, afr) (gnomAD).

What do computational predictors say about PLD1 p.Val1024Ile (c.3070G>A)?

AlphaMissense predicts likely benign (score 0.0569) — an in-silico prediction, not a clinical call.

PLD1 p.Val1024Ile

c.3070G>A · rs9827333 · VCV708886

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0569 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.07%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0569	likely benign
REVEL	0.137	moderately benign-leaning
SaProt	LLR -4.91	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.9	GERP -3.6
Regional constraint	o/e 0.98	unconstrained · MANE · 135 kb · p 0.57 · regional, not allelic
Overall
CADD	2.557	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.07% African / African-American · 1,556/75,046 alleles

Filtering AF 1.99% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.95%

Overall 0.294% 4,748/1,613,990 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.07%	48
Middle Eastern	0.396%	252
Remaining individualsnot grpmax-eligible	0.312%	320
Admixed American	0.265%	377
European (non-Finnish)	0.233%	429
South Asian	0.0659%	1,518
Finnishnot grpmax-eligible	0.00313%	31,998
East Asian	0.00223%	44,878

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: PLD1
Protein: p.Val1024Ile
Coding: c.3070G>A
MANE Select: NM_002662
dbSNP: rs9827333
Type: single nucleotide variant
Location: chr3:171603233 (GRCh38)
Gene constraint: LOEUF 0.822 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.92 · 2 PDB
Residue 1024: a UniProt-annotated variant site (in)

Full PLD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PLD1 c.2430-1G>A Pathogenic/Likely pathogenic ★★ same type
PLD1 c.2593+1G>A Pathogenic/Likely pathogenic ★★ same type
PLD1 p.Arg407Ter Pathogenic/Likely pathogenic ★★ same type
PLD1 p.Tyr894Ser Likely pathogenic ★★ same type
PLD1 p.Ala689Val Uncertain significance ★★ ⚠ same type
PLD1 p.Ala765Thr Uncertain significance ★★ ⚠ same type
PLD1 p.Arg172Lys Uncertain significance ★★ ⚠ same type
PLD1 p.Arg298Gln 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/pld1-p-val1024ile (accessed [today's date]).

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