Is ALG10 p.Val118= (c.354A>G) pathogenic?

ALG10 p.Val118= (c.354A>G) is classified Likely benign in ALG10 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-07). Common (popmax 13%, afr) — too common for a highly-penetrant pathogenic allele; Associated with ALG10-related disorder.

What condition is associated with ALG10 p.Val118= (c.354A>G)?

ALG10 p.Val118= (c.354A>G) is associated with ALG10-related disorder (ClinVar).

ALG10 p.Val118=

Q: How common is ALG10 p.Val118= (c.354A>G) in the general population?

ALG10 p.Val118= (c.354A>G) is common (popmax 13%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.354A>G · rs56393741 · VCV3057080

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 13%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

ALG10-related disorder

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 -0.45	GERP -5.9
Overall
CADD	3.808	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 13% African / African-American · 9,761/75,008 alleles

Filtering AF 12.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 12.7%

Overall 0.7% 11,295/1,614,116 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	13%	8
Admixed American	0.944%	106
Remaining individualsnot grpmax-eligible	0.872%	115
Middle Eastern	0.478%	209
Ashkenazi Jewishnot grpmax-eligible	0.0405%	2,467
European (non-Finnish)	0.031%	3,224
South Asian	0.0165%	6,073

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: ALG10
Protein: p.Val118=
Coding: c.354A>G
MANE Select: NM_032834
dbSNP: rs56393741
Type: single nucleotide variant
Location: chr12:34024144 (GRCh38)
Gene constraint: LOEUF 0.901 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.51

Full ALG10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG10-related disorder

Similar variants

ALG10 p.Leu456= Likely benign same condition
ALG10 p.Ser243= Benign ★★ same type
ALG10 p.Thr134= Benign ★★ same type
ALG10 p.Val269Ile Benign ★★ same type
ALG10 c.369+1G>T Likely pathogenic ★ same type
ALG10 p.Met61Val Likely pathogenic ★ ⚠ same type
ALG10 p.Ala11Asp Uncertain significance ★ ⚠ same type
ALG10 p.Ala11Thr 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/alg10-p-val118 (accessed [today's date]).

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