Is ALLC p.Asp171Glu (c.513T>A) pathogenic?

ALLC p.Asp171Glu (c.513T>A) is classified Uncertain significance in ALLC (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-23). AlphaMissense: likely pathogenic (0.6792); Absent from gnomAD v4.1.

How common is ALLC p.Asp171Glu (c.513T>A) in the general population?

ALLC p.Asp171Glu (c.513T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ALLC p.Asp171Glu (c.513T>A)?

AlphaMissense predicts likely pathogenic (score 0.6792) — an in-silico prediction, not a clinical call.

ALLC p.Asp171Glu

c.513T>A · rs780830343 · VCV2262238

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6792 · 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	0.6792	likely pathogenic
REVEL	0.58	indeterminate
SaProt	LLR -10.87	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	Δ0.48	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -2.9	GERP -4.1
Regional constraint	o/e 0.99	unconstrained · MANE · 31 kb · p 0.82 · regional, not allelic
Overall
CADD	22.9	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: ALLC
Protein: p.Asp171Glu
Coding: c.513T>A
MANE Select: NM_018436
dbSNP: rs780830343
Type: single nucleotide variant
Location: chr2:3695718 (GRCh38)
Gene constraint: LOEUF 1.144 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.83

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

Similar variants

ALLC p.Arg265Gln Benign ★★ ⚠ same type
ALLC p.Cys290Arg Benign ★★ same type
ALLC p.Ala125Ser Uncertain significance ★ ⚠ same type
ALLC p.Ala202Thr Uncertain significance ★ ⚠ same type
ALLC p.Ala95Glu Uncertain significance ★ ⚠ same type
ALLC p.Arg242Gln Uncertain significance ★ ⚠ same type
ALLC p.Arg242Trp Uncertain significance ★ ⚠ same type
ALLC p.Arg274Pro 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/allc-p-asp171glu (accessed [today's date]).

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