Is PARP3 p.Arg47= (c.141C>T) pathogenic?

PARP3 p.Arg47= (c.141C>T) is classified Benign in PARP3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-05-30). Common (popmax 7.13%, afr) — too common for a highly-penetrant pathogenic allele.

PARP3 p.Arg47=

Q: How common is PARP3 p.Arg47= (c.141C>T) in the general population?

PARP3 p.Arg47= (c.141C>T) is common (popmax 7.13%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.141C>T · rs112817696 · VCV788969

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 7.13%, afr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -5.1	GERP -3.4
Overall
CADD	1.49	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.13% African / African-American · 5,341/74,960 alleles

Filtering AF 6.97% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.9%

Overall 0.396% 6,375/1,611,024 alleles · common exomes 3,216/1,458,774 · genomes 3,159/152,250 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.13%	14
Admixed American	0.668%	150
Remaining individualsnot grpmax-eligible	0.556%	180
Middle Eastern	0.33%	303
South Asian	0.0265%	3,774
European (non-Finnish)	0.0205%	4,872
Ashkenazi Jewishnot grpmax-eligible	0.00677%	14,762

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: PARP3
Protein: p.Arg47=
Coding: c.141C>T
MANE Select: NM_001003931
dbSNP: rs112817696
Type: single nucleotide variant
Location: chr3:51943496 (GRCh38)
Gene constraint: LOEUF 1.001 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.68 · 16 PDB

Full PARP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PARP3 p.Ala41Ser Benign ★★ same type
PARP3 p.Gly385Ser Benign ★★ ⚠ same type
PARP3 p.Ile153= Likely benign ★★ same type
PARP3 p.Ala227Thr Uncertain significance ★ ⚠ same type
PARP3 p.Ala290Val Uncertain significance ★ ⚠ same type
PARP3 p.Ala295Asp Uncertain significance ★ same type
PARP3 p.Ala33Gly Uncertain significance ★ ⚠ same type
PARP3 p.Ala35Thr 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/parp3-p-arg47 (accessed [today's date]).

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