Is ABL1 p.Pro899Leu (c.2696C>T) pathogenic?

ABL1 p.Pro899Leu (c.2696C>T) is classified Benign/Likely benign in ABL1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-07-21). AlphaMissense: likely benign (0.1578); Very rare (popmax 0.004%, afr).

How common is ABL1 p.Pro899Leu (c.2696C>T) in the general population?

ABL1 p.Pro899Leu (c.2696C>T) is very rare (popmax 0.004%, afr) (gnomAD).

What do computational predictors say about ABL1 p.Pro899Leu (c.2696C>T)?

AlphaMissense predicts likely benign (score 0.1578) — an in-silico prediction, not a clinical call.

ABL1 p.Pro899Leu

c.2696C>T · rs777134913 · VCV2659613

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1578 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.004%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1578	likely benign
REVEL	0.216	benign-leaning
SaProt	LLR -9.44	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 7.5	GERP 1.4, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 5,156 bp · p 0.054 · regional, not allelic
Overall
CADD	24.7	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 0.004% African / African-American · 3/75,024 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000494%

Overall 0.00168% 27/1,610,980 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0339%	2,951
African / African-Americangrpmax	0.004%	25,008
Admixed American	0.00334%	29,906
Remaining individualsnot grpmax-eligible	0.00321%	31,159
East Asian	0.00223%	44,810
South Asian	0.0022%	45,462
Finnishnot grpmax-eligible	0.00161%	62,302
European (non-Finnish)	0.000509%	196,552

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro899Leu
Coding: c.2696C>T
MANE Select: NM_005157
dbSNP: rs777134913
Type: single nucleotide variant
Location: chr9:130884986 (GRCh38)
Gene constraint: LOEUF 0.19 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.68 · 85 PDB
Residue 899: the 'disordered' region; the 'dna-binding' region

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

Similar variants

ABL1 p.Pro899= Benign ★ same residue
ABL1 p.Pro899Ser Likely benign ★ ⚠ same residue
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

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-pro899leu (accessed [today's date]).

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