Is ALG13 p.Ala532= (c.1596G>A) pathogenic?

ALG13 p.Ala532= (c.1596G>A) is classified Likely benign in ALG13 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-03-03). Ultra-rare (popmax 0.0127%, sas); Associated with Inborn genetic diseases.

What condition is associated with ALG13 p.Ala532= (c.1596G>A)?

ALG13 p.Ala532= (c.1596G>A) is associated with Inborn genetic diseases, developmental and epileptic encephalopathy, 36 (ClinVar).

How common is ALG13 p.Ala532= (c.1596G>A) in the general population?

ALG13 p.Ala532= (c.1596G>A) is ultra-rare (popmax 0.0127%, sas) (gnomAD).

ALG13 p.Ala532=

c.1596G>A · rs891310320 · VCV771074

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0127%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP 2.9, phastCons 1
Overall
CADD	5.574	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0127% South Asian · 6/47,169 alleles

Filtering AF 0.00546% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00369%

Overall 0.00236% 26/1,101,075 alleles · ultra-rare exomes 24/989,461 · genomes 2/111,614 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0127%	7,862
African / African-American	0.00737%	13,561
Remaining individualsnot grpmax-eligible	0.00229%	43,745
European (non-Finnish)	0.00183%	54,559

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: ALG13
Protein: p.Ala532=
Coding: c.1596G>A
MANE Select: NM_001099922
dbSNP: rs891310320
Type: single nucleotide variant
Location: chrX:111723893 (GRCh38)
Structure: AlphaFold pLDDT 54.42
Residue 532: the tudor domain

Full ALG13 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

Also linked: developmental and epileptic encephalopathy, 36

Similar variants

ALG13 p.Asn107Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
ALG13 c.2458-1G>A Uncertain significance ★★ same condition
ALG13 c.2695+4G>A Uncertain significance ★★ same condition
ALG13 c.2932+6T>C Uncertain significance ★★ same condition
ALG13 c.834+3A>G Uncertain significance ★★ same condition
ALG13 c.932+2T>C Uncertain significance ★★ same condition
ALG13 p.Ala1044Thr Uncertain significance ★★ ⚠ same condition
ALG13 p.Ala173Val 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/alg13-p-ala532 (accessed [today's date]).

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