Is ASL p.Val455Gly (c.1364T>G) pathogenic?

ASL p.Val455Gly (c.1364T>G) is classified Uncertain significance in ASL (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-20). AlphaMissense: likely benign (0.2156); Very rare (popmax 0.00133%, afr); Associated with Inborn genetic diseases.

What condition is associated with ASL p.Val455Gly (c.1364T>G)?

ASL p.Val455Gly (c.1364T>G) is associated with Inborn genetic diseases (ClinVar).

How common is ASL p.Val455Gly (c.1364T>G) in the general population?

ASL p.Val455Gly (c.1364T>G) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about ASL p.Val455Gly (c.1364T>G)?

AlphaMissense predicts likely benign (score 0.2156) — an in-silico prediction, not a clinical call.

ASL p.Val455Gly

c.1364T>G · VCV4155079

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2156 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2156	likely benign
REVEL	0.772	pathogenic-leaning
SaProt	LLR -10.86	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	Δ0.65	donor loss, 2 bp away · masked 0 · deltas
Pangolin	Δ0.26	gain · loss 0.00 · SpliceAI calls loss · independent
Constraint at this position
Conservation	phyloP 7.6	GERP 4.4, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 17 kb · p 0.00078 · regional, not allelic
Overall
CADD	24.9	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 0.00133% African / African-American · 1/75,052 alleles

Overall 6.86e-05% 1/1,458,764 alleles · very rare

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: ASL
Protein: p.Val455Gly
Coding: c.1364T>G
MANE Select: NM_000048
Type: single nucleotide variant
Location: chr7:66092881 (GRCh38)
Gene constraint: LOEUF 0.937 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 96.51 · 2 PDB
Residue 455: an α-helix

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ASL p.Arg186Gln Pathogenic ★★ ⚠ same condition
ASL p.Ala26Thr Uncertain significance ★★ ⚠ same condition
ASL p.Ala2Asp Uncertain significance ★★ ⚠ same condition
ASL p.Arg151His Uncertain significance ★★ ⚠ same condition
ASL p.Arg32Trp Uncertain significance ★★ ⚠ same condition
ASL p.Val196Ile Uncertain significance ★★ ⚠ same condition
ASL c.348+5T>C Uncertain significance ★ same condition
ASL p.Arg141Lys Uncertain significance ★ ⚠ same condition

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/asl-p-val455gly (accessed [today's date]).

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