Is ABLIM1 p.Ser367Leu (c.1100C>T) pathogenic?

ABLIM1 p.Ser367Leu (c.1100C>T) is classified Uncertain significance in ABLIM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-06). AlphaMissense: likely pathogenic (0.6922); Absent from gnomAD v4.1.

How common is ABLIM1 p.Ser367Leu (c.1100C>T) in the general population?

ABLIM1 p.Ser367Leu (c.1100C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABLIM1 p.Ser367Leu (c.1100C>T)?

AlphaMissense predicts likely pathogenic (score 0.6922) — an in-silico prediction, not a clinical call.

ABLIM1 p.Ser367Leu

c.1100C>T · rs2507322474 · VCV2281368

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6922 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6922	likely pathogenic
REVEL	0.51	indeterminate
SaProt	LLR -11.59	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 124 kb · p 2.2e-08 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ABLIM1
Protein: p.Ser367Leu
Coding: c.1100C>T
MANE Select: NM_002313
dbSNP: rs2507322474
Type: single nucleotide variant
Location: chr10:114473898 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 59.86
Residue 367: a modified residue (phosphoserine); 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-ser367leu (accessed [today's date]).

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