Is ALG9 c.*1671T>C pathogenic?

ALG9 c.1671T>C is classified Benign in ALG9 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Low-frequency (popmax 4.11%, afr); Associated with ALG9-congenital disorder of glycosylation.

What condition is associated with ALG9 c.*1671T>C?

ALG9 c.*1671T>C is associated with ALG9-congenital disorder of glycosylation (ClinVar).

How common is ALG9 c.*1671T>C in the general population?

ALG9 c.*1671T>C is low-frequency (popmax 4.11%, afr) (gnomAD).

How is ALG9-CDG inherited?

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

ALG9 c.*1671T>C

rs116003998 · VCV880136

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 4.11%, afr)

Conditions

ALG9-congenital disorder of glycosylation

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 0.77	GERP -0.6, phastCons 0.002
Non-coding constraint	Z 1.99	1 kb window · o/e 0.86 · regional · uncalibrated
Overall
CADD	4.606	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.11% African / African-American · 1,706/41,542 alleles

Filtering AF 3.94% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.88%

Overall 1.19% 1,818/152,290 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.11%	24
Remaining individualsnot grpmax-eligible	1.28%	78
Admixed American	0.523%	191
Middle Eastern	0.34%	294
European (non-Finnish)	0.00588%	17,009

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: ALG9
Coding: c.*1671T>C
MANE Select: NM_024740
dbSNP: rs116003998
Type: single nucleotide variant
Location: chr11:111784726 (GRCh38)
Gene constraint: LOEUF 0.853 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.35 · 2 PDB

Full ALG9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG9-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG9-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Infancy, Neonatal

Similar variants

ALG9 c.566-1G>A Pathogenic/Likely pathogenic ★★ same condition
ALG9 c.896-2A>G Likely pathogenic ★★ same condition
ALG9 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same condition
ALG9 p.Trp248Ter Pathogenic/Likely pathogenic ★★ same condition
ALG9 p.Tyr287Cys Pathogenic/Likely pathogenic ★★ same condition
ALG9 c.*1607C>T Uncertain significance ★★ same condition
ALG9 c.*1624A>C Uncertain significance ★★ same condition
ALG9 c.*1722C>T 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/alg9-c-star-1671t-c (accessed [today's date]).

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