Is UTP14C p.Leu279= (c.835C>T) pathogenic?

UTP14C p.Leu279= (c.835C>T) is classified Benign in UTP14C (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-06-09). Common (popmax 70.4%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with ALG11-congenital disorder of glycosylation.

What condition is associated with UTP14C p.Leu279= (c.835C>T)?

UTP14C p.Leu279= (c.835C>T) is associated with ALG11-congenital disorder of glycosylation (ClinVar).

How is ALG11-CDG inherited?

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

UTP14C p.Leu279=

Q: How common is UTP14C p.Leu279= (c.835C>T) in the general population?

UTP14C p.Leu279= (c.835C>T) is common (popmax 70.4%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.835C>T · rs3742291 · VCV312426

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 70.4%, nfe) — too common for a highly-penetrant pathogenic allele

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 -6.6	GERP -3.7
Overall
CADD	0.245	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 70.4% European (non-Finnish) · 831,242/1,179,996 alleles

Filtering AF 70.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 70.3%

Overall 66.7% 1,076,058/1,613,934 alleles · common exomes 989,145/1,461,868 · genomes 86,913/152,066 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	70.4%	1
Finnishnot grpmax-eligible	70.1%	1
Middle Eastern	69.3%	1
Remaining individualsnot grpmax-eligible	66%	2
Admixed American	65.5%	2
Amishnot grpmax-eligible	63.5%	2
Ashkenazi Jewishnot grpmax-eligible	63.2%	2
East Asian	56.7%	2
South Asian	54.5%	2
African / African-American	27.7%	4

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.Leu279=
Coding: c.835C>T
MANE Select: NM_021645
dbSNP: rs3742291
Type: single nucleotide variant
Location: chr13:52029639 (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-leu279 (accessed [today's date]).

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