Is ABLIM3 p.Ser84Asn (c.251G>A) pathogenic?

ABLIM3 p.Ser84Asn (c.251G>A) is classified Uncertain significance in ABLIM3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-11). AlphaMissense: ambiguous (0.346); Very rare (popmax 0.00333%, amr).

How common is ABLIM3 p.Ser84Asn (c.251G>A) in the general population?

ABLIM3 p.Ser84Asn (c.251G>A) is very rare (popmax 0.00333%, amr) (gnomAD).

What do computational predictors say about ABLIM3 p.Ser84Asn (c.251G>A)?

AlphaMissense predicts ambiguous (score 0.346) — an in-silico prediction, not a clinical call.

ABLIM3 p.Ser84Asn

c.251G>A · rs750610592 · VCV3132300

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.346 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00333%, amr)

Computational evidence

Protein change
AlphaMissense	0.346	ambiguous
REVEL	0.434	indeterminate
SaProt	LLR -8.28	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.7, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 116 kb · p 0.0017 · regional, not allelic
Overall
CADD	28.6	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 0.00333% Admixed American · 2/60,026 alleles

Filtering AF 0.000553% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000207%

Overall 0.000752% 11/1,461,870 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0141%	7,116
Admixed Americangrpmax	0.00333%	30,013

Finnish 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: ABLIM3
Protein: p.Ser84Asn
Coding: c.251G>A
MANE Select: NM_014945
dbSNP: rs750610592
Type: single nucleotide variant
Location: chr5:149198318 (GRCh38)
Gene constraint: LOEUF 0.691 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.31 · 2 PDB
Residue 84: the lim zinc-binding 2 domain

Full ABLIM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABLIM3 p.Arg513Cys Uncertain significance ★★ ⚠ same type
ABLIM3 p.Ala166Gly Uncertain significance ★ ⚠ same type
ABLIM3 p.Ala297Val Uncertain significance ★ ⚠ same type
ABLIM3 p.Ala371Asp Uncertain significance ★ ⚠ same type
ABLIM3 p.Ala600Pro Uncertain significance ★ ⚠ same type
ABLIM3 p.Arg15Trp Uncertain significance ★ ⚠ same type
ABLIM3 p.Arg215Gln Uncertain significance ★ ⚠ same type
ABLIM3 p.Arg238Cys 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/ablim3-p-ser84asn (accessed [today's date]).

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