Is ALG6 c.816+11del pathogenic?

ALG6 c.816+11del is classified Likely benign in ALG6 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-23). Very rare (popmax 8.47e-05%, nfe); Associated with ALG6-congenital disorder of glycosylation 1C.

What condition is associated with ALG6 c.816+11del?

ALG6 c.816+11del is associated with ALG6-congenital disorder of glycosylation 1C (ClinVar).

How common is ALG6 c.816+11del in the general population?

ALG6 c.816+11del is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is ALG6-CDG inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ALG6 c.816+11del

rs1644519196 · VCV2056101

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

ALG6-congenital disorder of glycosylation 1C

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +11	near-intronic (+11 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.25	GERP -3.4
Non-coding constraint	Z 3.27	1 kb window · o/e 0.75 · regional · uncalibrated

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,179,954 alleles

Overall 6.84e-05% 1/1,461,714 alleles · very rare

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: ALG6
Coding: c.816+11del
MANE Select: NM_013339
dbSNP: rs1644519196
Type: Deletion
Location: chr1:63412070 (GRCh38)
Gene constraint: LOEUF 0.892 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.08

Full ALG6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG6-congenital disorder of glycosylation 1C — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG6-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ALG6 c.82_82+8del Likely pathogenic ★★ same condition
ALG6 p.Asn283fs Pathogenic/Likely pathogenic ★★ same condition
ALG6 p.Gln417fs Pathogenic/Likely pathogenic ★★ same condition
ALG6 p.Leu416fs Pathogenic/Likely pathogenic ★★ same condition
ALG6 p.Met34fs Pathogenic/Likely pathogenic ★★ same condition
ALG6 p.Phe228fs Pathogenic/Likely pathogenic ★★ same condition
ALG6 p.Phe336fs Pathogenic/Likely pathogenic ★★ same condition
ALG6 p.Pro379fs Pathogenic/Likely pathogenic ★★ 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/alg6-c-816-plus-11del (accessed [today's date]).

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