Is ABL2 p.Gln15Ter (c.43C>T) pathogenic?

ABL2 p.Gln15Ter (c.43C>T) is classified Uncertain significance in ABL2 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-09-08). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ABL2 p.Gln15Ter (c.43C>T)?

ABL2 p.Gln15Ter (c.43C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ABL2 p.Gln15Ter (c.43C>T) in the general population?

ABL2 p.Gln15Ter (c.43C>T) is absent from gnomAD v4.1 (gnomAD).

ABL2 p.Gln15Ter

c.43C>T · rs1553236156 · VCV521879

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,576,784)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 12
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.4, phastCons 1
Overall
CADD	38.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,576,784). 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: ABL2
Protein: p.Gln15Ter
Coding: c.43C>T
MANE Select: NM_007314
dbSNP: rs1553236156
Type: single nucleotide variant
Location: chr1:179229355 (GRCh38)
Gene constraint: LOEUF 0.578 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.19 · 9 PDB
Residue 15: the 'disordered' region; the 'cap' region

Full ABL2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABL2 p.Gln15His Uncertain significance ★ ⚠ same residue
ABL2 p.Ser249Phe Uncertain significance ★ ⚠ same condition
ABL2 c.*4125A>G Benign ★★ same type
ABL2 p.Lys930Arg Benign ★★ same type
ABL2 p.Thr784Ser Likely benign ★★ same type
ABL2 p.Ala1029Thr Uncertain significance ★ ⚠ same type
ABL2 p.Ala1076Thr Uncertain significance ★ ⚠ same type
ABL2 p.Ala1156Val 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/abl2-p-gln15ter (accessed [today's date]).

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