Is UNG p.Pro22Leu (c.65C>T) pathogenic?

UNG p.Pro22Leu (c.65C>T) is classified Uncertain significance in UNG (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-05-07). AlphaMissense: likely benign (0.0737); Very rare (popmax 0.00499%, nfe); Associated with hyper-IgM syndrome type 5.

What condition is associated with UNG p.Pro22Leu (c.65C>T)?

UNG p.Pro22Leu (c.65C>T) is associated with hyper-IgM syndrome type 5 (ClinVar).

How common is UNG p.Pro22Leu (c.65C>T) in the general population?

UNG p.Pro22Leu (c.65C>T) is very rare (popmax 0.00499%, nfe) (gnomAD).

What do computational predictors say about UNG p.Pro22Leu (c.65C>T)?

AlphaMissense predicts likely benign (score 0.0737) — an in-silico prediction, not a clinical call.

UNG p.Pro22Leu

c.65C>T · rs373668102 · VCV880878

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0737 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00499%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hyper-IgM syndrome type 5

Computational evidence

Protein change
AlphaMissense	0.0737	likely benign
REVEL	0.081	moderately benign-leaning
SaProt	LLR -7.94	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP -0.005, phastCons 0.99
Regional constraint	o/e 0.98	unconstrained · MANE · 12 kb · p 0.74 · regional, not allelic
Overall
CADD	10.03	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.00499% European (non-Finnish) · 58/1,162,794 alleles

Filtering AF 0.00391% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00358%

Overall 0.0038% 60/1,579,058 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00499%	20,048
Remaining individualsnot grpmax-eligible	0.00164%	61,032
African / African-American	0.00136%	73,786

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: UNG
Protein: p.Pro22Leu
Coding: c.65C>T
MANE Select: NM_080911
dbSNP: rs373668102
Type: single nucleotide variant
Location: chr12:109097744 (GRCh38)
Gene constraint: LOEUF 1.22 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.52 · 24 PDB
Residue 22: the 'disordered' region; the 'interaction with fam72a' region; the 'mitochondrial localization signal' region

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

Disease context

hyper-IgM syndrome type 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

UNG c.623-9T>A Uncertain significance ★★ same condition
UNG c.801+5G>A Uncertain significance ★★ same condition
UNG p.Ala21Thr Uncertain significance ★★ ⚠ same condition
UNG p.Ala87Val Uncertain significance ★★ ⚠ same condition
UNG p.Arg122Ser Uncertain significance ★★ ⚠ same condition
UNG p.Arg269Trp Uncertain significance ★★ ⚠ same condition
UNG p.Asn77Lys Uncertain significance ★★ ⚠ same condition
UNG p.Gln133His 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/ung-p-pro22leu (accessed [today's date]).

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