Is PARP14 p.Gln1413Pro (c.4238A>C) pathogenic?

PARP14 p.Gln1413Pro (c.4238A>C) is classified Benign in PARP14 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). AlphaMissense: likely benign (0.054); Low-frequency (popmax 2.37%, afr).

How common is PARP14 p.Gln1413Pro (c.4238A>C) in the general population?

PARP14 p.Gln1413Pro (c.4238A>C) is low-frequency (popmax 2.37%, afr) (gnomAD).

What do computational predictors say about PARP14 p.Gln1413Pro (c.4238A>C)?

AlphaMissense predicts likely benign (score 0.054) — an in-silico prediction, not a clinical call.

PARP14 p.Gln1413Pro

c.4238A>C · rs61732768 · VCV787256

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.054 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.37%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.054	likely benign
REVEL	0.022	moderately benign-leaning
SaProt	LLR -5.48	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 -8.4	GERP -4.2
Regional constraint	o/e 0.83	unconstrained · MANE · 47 kb · p 1.1e-13 · regional, not allelic
Overall
CADD	0.002	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 2.37% African / African-American · 1,778/74,902 alleles

Filtering AF 2.28% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.24%

Overall 0.189% 3,055/1,612,276 alleles · low-frequency exomes 1,981/1,460,014 · genomes 1,074/152,262 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.37%	42
Middle Eastern	0.858%	117
Remaining individualsnot grpmax-eligible	0.341%	293
Admixed American	0.333%	300
Ashkenazi Jewishnot grpmax-eligible	0.132%	758
European (non-Finnish)	0.0608%	1,645
South Asian	0.0531%	1,884
Finnishnot grpmax-eligible	0.0141%	7,111

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: PARP14
Protein: p.Gln1413Pro
Coding: c.4238A>C
MANE Select: NM_017554
dbSNP: rs61732768
Type: single nucleotide variant
Location: chr3:122718389 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.00 · 47 PDB

Full PARP14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PARP14 p.Pro1200Leu Uncertain significance ★★ ⚠ same type
PARP14 p.Ala1513Val Benign ★★ same type
PARP14 p.Ala864= Benign ★★ same type
PARP14 p.Asp488Asn Benign ★★ same type
PARP14 p.Ala1187Ser Uncertain significance ★ ⚠ same type
PARP14 p.Ala1202Ser Uncertain significance ★ ⚠ same type
PARP14 p.Ala1350Asp Uncertain significance ★ ⚠ same type
PARP14 p.Ala385Ser 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/parp14-p-gln1413pro (accessed [today's date]).

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