Is ABL1 p.Val959fs (c.2874del) pathogenic?

ABL1 p.Val959fs (c.2874del) is classified Uncertain significance in ABL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-07). Absent from gnomAD.

How common is ABL1 p.Val959fs (c.2874del) in the general population?

ABL1 p.Val959fs (c.2874del) is absent from gnomAD (gnomAD).

ABL1 p.Val959fs

c.2874del · rs2490752900 · VCV2853282

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	escapes	premature termination codon in the last exon (11 of 11) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2	GERP -0.65, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: ABL1
Protein: p.Val959fs
Coding: c.2874del
MANE Select: NM_005157
dbSNP: rs2490752900
Type: Deletion
Location: chr9:130885162 (GRCh38)
Gene constraint: LOEUF 0.19 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.68 · 85 PDB
Residue 959: the 'disordered' region; the 'dna-binding' region; the 'f-actin-binding' region

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

Similar variants

ABL1 p.Val959Met Benign/Likely benign ★★ ⚠ same residue
ABL1 c.1679-3del Uncertain significance ★ same type
ABL1 p.Asp276fs Uncertain significance ★ same type
ABL1 p.Asp391fs Uncertain significance ★ same type
ABL1 p.Gln627fs Uncertain significance ★ same type
ABL1 p.Glu549fs Uncertain significance ★ same type
ABL1 p.Gly864fs Uncertain significance ★ same type
ABL1 p.Ile360fs 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/abl1-p-val959fs (accessed [today's date]).

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