Is ALG13 p.Arg36= (c.108A>G) pathogenic?

ALG13 p.Arg36= (c.108A>G) is classified Benign/Likely benign in ALG13 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-11-17). Rare (popmax 0.258%, mid); Associated with Inborn genetic diseases.

What condition is associated with ALG13 p.Arg36= (c.108A>G)?

ALG13 p.Arg36= (c.108A>G) is associated with Inborn genetic diseases, developmental and epileptic encephalopathy, 36 (ClinVar).

How common is ALG13 p.Arg36= (c.108A>G) in the general population?

ALG13 p.Arg36= (c.108A>G) is rare (popmax 0.258%, mid) (gnomAD).

ALG13 p.Arg36=

c.108A>G · rs769838471 · VCV509168

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.258%, mid)

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 0.19	GERP -3, phastCons 0.24
Overall
CADD	9.018	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.258% Middle Eastern · 11/4,268 alleles

Filtering AF 0.179% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.167%

Overall 0.0202% 241/1,191,282 alleles · rare exomes 231/1,080,057 · genomes 10/111,225 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.258%	388
South Asian	0.211%	475
Remaining individualsnot grpmax-eligible	0.0257%	3,898
European (non-Finnish)	0.0115%	8,700
Admixed American	0.00472%	21,200
African / African-American	0.00356%	28,052

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.Arg36=
Coding: c.108A>G
MANE Select: NM_001099922
dbSNP: rs769838471
Type: single nucleotide variant
Location: chrX:111682158 (GRCh38)
Structure: AlphaFold pLDDT 54.42
Residue 36: the 'glycosyltransferase activity' region

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.Arg36Ter Uncertain significance ★ same residue
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

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-arg36 (accessed [today's date]).

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