Is ALG13 p.Gln147Arg (c.440A>G) pathogenic?

ALG13 p.Gln147Arg (c.440A>G) is classified Uncertain significance in ALG13 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-21). AlphaMissense: likely benign (0.0748); No allele count reported in gnomAD v4.1 (AN 1,211,165).

How common is ALG13 p.Gln147Arg (c.440A>G) in the general population?

ALG13 p.Gln147Arg (c.440A>G) is no allele count reported in gnomAD v4.1 (AN 1,211,165) (gnomAD).

What do computational predictors say about ALG13 p.Gln147Arg (c.440A>G)?

AlphaMissense predicts likely benign (score 0.0748) — an in-silico prediction, not a clinical call.

ALG13 p.Gln147Arg

c.440A>G · rs2147996000 · VCV1313388

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0748 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,211,165)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0748	likely benign
REVEL	0.069	moderately benign-leaning
SaProt	LLR -5.45	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.8	GERP 2.7, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 27 kb · p 0.23 · regional, not allelic
Overall
CADD	18.37	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

No allele count reported in gnomAD v4.1 (AN 1,211,165). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ALG13
Protein: p.Gln147Arg
Coding: c.440A>G
MANE Select: NM_001099922
dbSNP: rs2147996000
Type: single nucleotide variant
Location: chrX:111708083 (GRCh38)
Structure: AlphaFold pLDDT 54.42
Residue 147: the 'deubiquitinase activity' region

Full ALG13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ALG13 p.Gln147= Likely benign ★ same residue
ALG13 p.Asn107Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
ALG13 c.2458-1G>A Uncertain significance ★★ same type
ALG13 c.2695+4G>A Uncertain significance ★★ same type
ALG13 c.2932+6T>C Uncertain significance ★★ same type
ALG13 c.834+3A>G Uncertain significance ★★ same type
ALG13 c.932+2T>C Uncertain significance ★★ same type
ALG13 p.Ala1044Thr 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/alg13-p-gln147arg (accessed [today's date]).

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