Is ABLIM1 p.Ile564Phe (c.1690A>T) pathogenic?

ABLIM1 p.Ile564Phe (c.1690A>T) is classified Uncertain significance in ABLIM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-20). AlphaMissense: likely benign (0.3185); Ultra-rare (popmax 0.0133%, amr).

How common is ABLIM1 p.Ile564Phe (c.1690A>T) in the general population?

ABLIM1 p.Ile564Phe (c.1690A>T) is ultra-rare (popmax 0.0133%, amr) (gnomAD).

What do computational predictors say about ABLIM1 p.Ile564Phe (c.1690A>T)?

AlphaMissense predicts likely benign (score 0.3185) — an in-silico prediction, not a clinical call.

ABLIM1 p.Ile564Phe

c.1690A>T · rs780288120 · VCV3131963

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3185 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.3185	likely benign
REVEL	0.405	indeterminate
SaProt	LLR -6.86	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>C here scores Δ0.25 · evaluated, not missing
Constraint at this position
Conservation	phyloP 6.2	GERP 1.4, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 6,313 bp · p 0.84 · regional, not allelic
Overall
CADD	24.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% Admixed American · 8/60,014 alleles

Filtering AF 0.00661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00482%

Overall 0.00142% 23/1,614,152 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0133%	7,502
European (non-Finnish)	0.00127%	78,668

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: ABLIM1
Protein: p.Ile564Phe
Coding: c.1690A>T
MANE Select: NM_002313
dbSNP: rs780288120
Type: single nucleotide variant
Location: chr10:114447925 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 59.86
Residue 564: the 'disordered' region

Full ABLIM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABLIM1 p.Ala506Thr Uncertain significance ★★ ⚠ same type
ABLIM1 c.2060-2A>G Uncertain significance ★ same type
ABLIM1 c.379+1G>A Uncertain significance ★ same type
ABLIM1 p.Ala29Val Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala51Thr Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala55Gly Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala83Val Uncertain significance ★ ⚠ same type
ABLIM1 p.Arg112Gln 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/ablim1-p-ile564phe (accessed [today's date]).

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