Is ABLIM1 p.Ile372Val (c.1114A>G) pathogenic?

ABLIM1 p.Ile372Val (c.1114A>G) is classified Uncertain significance in ABLIM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-28). AlphaMissense: ambiguous (0.4582); Very rare (popmax 0.00134%, afr).

How common is ABLIM1 p.Ile372Val (c.1114A>G) in the general population?

ABLIM1 p.Ile372Val (c.1114A>G) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about ABLIM1 p.Ile372Val (c.1114A>G)?

AlphaMissense predicts ambiguous (score 0.4582) — an in-silico prediction, not a clinical call.

ABLIM1 p.Ile372Val

c.1114A>G · VCV4636404

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4582 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4582	ambiguous
REVEL	0.233	benign-leaning
SaProt	LLR -7.46	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 2.3, phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 124 kb · p 2.2e-08 · regional, not allelic
Overall
CADD	26.3	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 0.00134% African / African-American · 1/74,834 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000186% 3/1,610,312 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00134%	74,834
European (non-Finnish)	0.00017%	588,367

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.Ile372Val
Coding: c.1114A>G
MANE Select: NM_002313
Type: single nucleotide variant
Location: chr10:114473884 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 59.86

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-ile372val (accessed [today's date]).

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