Is UTP14C p.Ser64= (c.192T>C) pathogenic?

UTP14C p.Ser64= (c.192T>C) is classified Conflicting classifications of pathogenicity in UTP14C (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-10-01). Ultra-rare (popmax 0.015%, amr); Associated with ALG11-congenital disorder of glycosylation.

What condition is associated with UTP14C p.Ser64= (c.192T>C)?

UTP14C p.Ser64= (c.192T>C) is associated with ALG11-congenital disorder of glycosylation (ClinVar).

How common is UTP14C p.Ser64= (c.192T>C) in the general population?

UTP14C p.Ser64= (c.192T>C) is ultra-rare (popmax 0.015%, amr) (gnomAD).

How is ALG11-CDG inherited?

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

UTP14C p.Ser64=

c.192T>C · rs137988059 · VCV312421

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.015%, amr)

Conditions

ALG11-congenital disorder of glycosylation

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.89	GERP -0.78, phastCons 0.01
Overall
CADD	4.582	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.015% Admixed American · 9/60,016 alleles

Filtering AF 0.00773% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00578%

Overall 0.00341% 55/1,614,140 alleles · ultra-rare exomes 51/1,461,894 · genomes 4/152,246 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.015%	6,668
Remaining individualsnot grpmax-eligible	0.0064%	15,622
European (non-Finnish)	0.00356%	28,096

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: UTP14C
Protein: p.Ser64=
Coding: c.192T>C
MANE Select: NM_021645
dbSNP: rs137988059
Type: single nucleotide variant
Location: chr13:52028996 (GRCh38)

Full UTP14C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG11-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG11-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

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/utp14c-p-ser64 (accessed [today's date]).

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