Is ABLIM2 p.Arg361Gln (c.1082G>A) pathogenic?

ABLIM2 p.Arg361Gln (c.1082G>A) is classified Uncertain significance in ABLIM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-04). AlphaMissense: likely benign (0.2097); Very rare (popmax 0.00709%, sas).

How common is ABLIM2 p.Arg361Gln (c.1082G>A) in the general population?

ABLIM2 p.Arg361Gln (c.1082G>A) is very rare (popmax 0.00709%, sas) (gnomAD).

What do computational predictors say about ABLIM2 p.Arg361Gln (c.1082G>A)?

AlphaMissense predicts likely benign (score 0.2097) — an in-silico prediction, not a clinical call.

ABLIM2 p.Arg361Gln

c.1082G>A · VCV3993924

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2097 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00709%, sas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2097	likely benign
REVEL	0.43	indeterminate
SaProt	LLR -7.91	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 1.9, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 192 kb · p 0.27 · regional, not allelic
Overall
CADD	33.0	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 0.00709% South Asian · 6/84,654 alleles

Filtering AF 0.00464% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00426%

Overall 0.00499% 78/1,562,040 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00709%	14,109
European (non-Finnish)	0.00581%	17,217
African / African-American	0.00408%	24,518
Remaining individualsnot grpmax-eligible	0.0033%	30,319

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: ABLIM2
Protein: p.Arg361Gln
Coding: c.1082G>A
MANE Select: NM_001130083
Type: single nucleotide variant
Location: chr4:8029742 (GRCh38)
Gene constraint: LOEUF 0.743 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.21 · 3 PDB
Residue 361: the 'disordered' region

Full ABLIM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABLIM2 p.Arg361Trp Uncertain significance ★ ⚠ same residue
ABLIM2 c.763+4C>T Benign ★★ same type
ABLIM2 c.763+5A>G Benign ★★ same type
ABLIM2 p.Ala144Thr Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala21Val Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala288Val Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala476Ser Uncertain significance ★ ⚠ same type
ABLIM2 p.Ala565Asp 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/ablim2-p-arg361gln (accessed [today's date]).

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