Is UBE2T p.Ser5= (c.15A>G) pathogenic?

UBE2T p.Ser5= (c.15A>G) is classified Benign in UBE2T (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-04). Common (popmax 59.7%, mid) — too common for a highly-penetrant pathogenic allele; Associated with Fanconi anemia complementation group T.

What condition is associated with UBE2T p.Ser5= (c.15A>G)?

UBE2T p.Ser5= (c.15A>G) is associated with Fanconi anemia complementation group T (ClinVar).

UBE2T p.Ser5=

Q: How common is UBE2T p.Ser5= (c.15A>G) in the general population?

UBE2T p.Ser5= (c.15A>G) is common (popmax 59.7%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.15A>G · rs14451 · VCV1269291

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 59.7%, mid) — too common for a highly-penetrant pathogenic allele

Conditions

Fanconi anemia complementation group T

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 -0.73	GERP -3.8, phastCons 0.018
Overall
CADD	5.841	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 59.7% Middle Eastern · 3,617/6,054 alleles

Filtering AF 58.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 57.5%

Overall 48.5% 781,587/1,612,872 alleles · common

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	60.5%	2
Amishnot grpmax-eligible	59.9%	2
Middle Easterngrpmax	59.7%	2
Finnishnot grpmax-eligible	52.8%	2
European (non-Finnish)	50.5%	2
Remaining individualsnot grpmax-eligible	48.5%	2
African / African-American	43.6%	2
South Asian	38.5%	3
Admixed American	31.4%	3
East Asian	29%	3

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: UBE2T
Protein: p.Ser5=
Coding: c.15A>G
MANE Select: NM_014176
dbSNP: rs14451
Type: single nucleotide variant
Location: chr1:202335740 (GRCh38)
Gene constraint: LOEUF 0.838 · pLI 0.08 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.36 · 13 PDB
Residue 5: the ubc core domain; an α-helix

Full UBE2T gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Fanconi anemia complementation group T — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

UBE2T c.385-11T>C Benign ★★ same condition
UBE2T p.Gln2Glu Pathogenic ★ ⚠ same condition
UBE2T c.-65+1729G>A Uncertain significance ★ same condition
UBE2T c.179+5G>A Pathogenic same condition
UBE2T p.Pro62fs Likely pathogenic ★ same condition
UBE2T c.110-280_468+264del Pathogenic same condition
UBE2T c.110-280_468+264dup Pathogenic same condition
UBE2T p.Ala143Thr Uncertain significance ★★ ⚠ same type

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/ube2t-p-ser5 (accessed [today's date]).

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