Is ALG14 p.Val141Gly (c.422T>G) pathogenic?

ALG14 p.Val141Gly (c.422T>G) is classified Uncertain significance in ALG14 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2024-05-29). AlphaMissense: likely pathogenic (0.8909); Ultra-rare (popmax 0.012%, nfe); Associated with Inborn genetic diseases.

How common is ALG14 p.Val141Gly (c.422T>G) in the general population?

ALG14 p.Val141Gly (c.422T>G) is ultra-rare (popmax 0.012%, nfe) (gnomAD).

What do computational predictors say about ALG14 p.Val141Gly (c.422T>G)?

AlphaMissense predicts likely pathogenic (score 0.8909) — an in-silico prediction, not a clinical call.

ALG14 p.Val141Gly

Q: What condition is associated with ALG14 p.Val141Gly (c.422T>G)?

ALG14 p.Val141Gly (c.422T>G) is associated with Inborn genetic diseases, congenital myasthenic syndrome 15, intellectual developmental disorder with epilepsy, behavioral abnormalities, and coarse facies (ClinVar).

c.422T>G · rs139005007 · VCV652328

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely pathogenic

0.8909 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.012%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8909	likely pathogenic
REVEL	0.866	moderately pathogenic-leaning
SaProt	LLR -16.21	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	Δ0.34	acceptor loss · deltas
Constraint at this position
Conservation	phyloP 11	GERP 2.3, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 90 kb · p 0.32 · regional, not allelic
Overall
CADD	25.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.012% European (non-Finnish) · 141/1,179,134 alleles

Filtering AF 0.0103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00973%

Overall 0.00912% 147/1,612,372 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.012%	8,363
Remaining individualsnot grpmax-eligible	0.00481%	20,809
Finnishnot grpmax-eligible	0.00313%	31,992
Admixed American	0.00167%	59,824

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: ALG14
Protein: p.Val141Gly
Coding: c.422T>G
MANE Select: NM_144988
dbSNP: rs139005007
Type: single nucleotide variant
Location: chr1:94983305 (GRCh38)
Gene constraint: LOEUF 1.055 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.06
Residue 141: a UniProt-annotated variant site (in cms15); a UniProt-annotated variant site (in mepca; uncertain significance; decreased function in dolichol-linked oligosaccharide biosynthetic process)

Full ALG14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: congenital myasthenic syndrome 15 intellectual developmental disorder with epilepsy, behavioral abnormalities, and coarse facies myopathy, epilepsy, and progressive cerebral atrophy

Similar variants

ALG14 p.Val141Met Uncertain significance ★ ⚠ same residue
ALG14 p.Val141= Likely benign ★ same residue
ALG14 p.Ala13Ser Uncertain significance ★★ ⚠ same condition
ALG14 p.Arg104Gln Uncertain significance ★★ ⚠ same condition
ALG14 p.Arg109Gln Uncertain significance ★★ ⚠ same condition
ALG14 p.Arg109Trp Uncertain significance ★★ ⚠ same condition
ALG14 p.Asn61Asp Uncertain significance ★★ ⚠ same condition
ALG14 p.Asn61Ser 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/alg14-p-val141gly (accessed [today's date]).

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