Is ABL1 p.Lys247Arg (c.740A>G) pathogenic?

ABL1 p.Lys247Arg (c.740A>G) is classified Benign/Likely benign in ABL1 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-01). AlphaMissense: likely benign (0.142); Rare (popmax 0.378%, nfe).

How common is ABL1 p.Lys247Arg (c.740A>G) in the general population?

ABL1 p.Lys247Arg (c.740A>G) is rare (popmax 0.378%, nfe) (gnomAD).

What do computational predictors say about ABL1 p.Lys247Arg (c.740A>G)?

AlphaMissense predicts likely benign (score 0.142) — an in-silico prediction, not a clinical call.

ABL1 p.Lys247Arg

c.740A>G · rs34549764 · VCV133450

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.142 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.378%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.142	likely benign
REVEL	0.069	moderately benign-leaning
SaProt	LLR -5.18	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 6	GERP 1.2, phastCons 1
Regional constraint	o/e 0.43	unconstrained · MANE · 10 kb · p 1.5e-16 · regional, not allelic
Overall
CADD	24.3	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 0.378% European (non-Finnish) · 4,455/1,180,030 alleles

Filtering AF 0.368% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.364%

Overall 0.308% 4,972/1,614,194 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.378%	265
Finnishnot grpmax-eligible	0.353%	283
Amishnot grpmax-eligible	0.329%	304
Remaining individualsnot grpmax-eligible	0.21%	477
Admixed American	0.145%	690
Ashkenazi Jewishnot grpmax-eligible	0.0473%	2,115
African / African-American	0.04%	2,502
South Asian	0.0274%	3,643
Middle Eastern	0.0165%	6,062

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: ABL1
Protein: p.Lys247Arg
Coding: c.740A>G
MANE Select: NM_005157
dbSNP: rs34549764
Type: single nucleotide variant
Location: chr9:130862953 (GRCh38)
Gene constraint: LOEUF 0.19 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.68 · 85 PDB
Residue 247: a β-strand; the protein kinase domain; a UniProt-annotated variant site (in)

Full ABL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABL1 p.Ala337Thr Pathogenic ★★ ⚠ same type
ABL1 p.Ala433Thr Likely pathogenic ★★ ⚠ same type
ABL1 p.Asp504Gly Likely pathogenic ★★ ⚠ same type
ABL1 p.Glu509Lys Pathogenic/Likely pathogenic ★★ same type
ABL1 p.Gly254Arg Pathogenic/Likely pathogenic ★★ same type
ABL1 p.Pro230Leu Likely pathogenic ★★ ⚠ same type
ABL1 p.Trp99Arg Likely pathogenic ★★ same type
ABL1 p.Tyr226Cys Pathogenic/Likely pathogenic ★★ ⚠ 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/abl1-p-lys247arg (accessed [today's date]).

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