Is ALG13 p.Tyr61= (c.183C>T) pathogenic?

ALG13 p.Tyr61= (c.183C>T) is classified Benign in ALG13 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-03). Low-frequency (popmax 1.75%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ALG13 p.Tyr61= (c.183C>T)?

ALG13 p.Tyr61= (c.183C>T) is associated with Inborn genetic diseases, developmental and epileptic encephalopathy, 36 (ClinVar).

How common is ALG13 p.Tyr61= (c.183C>T) in the general population?

ALG13 p.Tyr61= (c.183C>T) is low-frequency (popmax 1.75%, nfe) (gnomAD).

ALG13 p.Tyr61=

c.183C>T · rs146925326 · VCV238290

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.75%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.33	donor loss · deltas
Constraint at this position
Conservation	phyloP 0.76	GERP -1.6, phastCons 1
Overall
CADD	13.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.75% European (non-Finnish) · 15,554/888,179 alleles

Filtering AF 1.73% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.72%

Overall 1.41% 16,893/1,197,624 alleles · low-frequency exomes 15,858/1,085,509 · genomes 1,035/112,115 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	1.75%	57
Remaining individualsnot grpmax-eligible	1.2%	83
Finnishnot grpmax-eligible	0.886%	113
Admixed American	0.284%	352
African / African-American	0.211%	474
Ashkenazi Jewishnot grpmax-eligible	0.207%	482
South Asian	0.129%	777
Middle Eastern	0.0466%	2,148

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.Tyr61=
Coding: c.183C>T
MANE Select: NM_001099922
dbSNP: rs146925326
Type: single nucleotide variant
Location: chrX:111682233 (GRCh38)
Structure: AlphaFold pLDDT 54.42
Residue 61: 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.Tyr61Asp 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-tyr61 (accessed [today's date]).

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