Is UBAP1 p.Ala152Val (c.455C>T) pathogenic?

UBAP1 p.Ala152Val (c.455C>T) is classified Uncertain significance in UBAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-17). AlphaMissense: likely benign (0.1702); Very rare (popmax 0.00667%, afr); Associated with Inborn genetic diseases.

What condition is associated with UBAP1 p.Ala152Val (c.455C>T)?

UBAP1 p.Ala152Val (c.455C>T) is associated with Inborn genetic diseases (ClinVar).

How common is UBAP1 p.Ala152Val (c.455C>T) in the general population?

UBAP1 p.Ala152Val (c.455C>T) is very rare (popmax 0.00667%, afr) (gnomAD).

What do computational predictors say about UBAP1 p.Ala152Val (c.455C>T)?

AlphaMissense predicts likely benign (score 0.1702) — an in-silico prediction, not a clinical call.

UBAP1 p.Ala152Val

c.455C>T · VCV3976638

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1702 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00667%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1702	likely benign
REVEL	0.167	moderately benign-leaning
SaProt	LLR -5.57	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 4.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.21	constrained · MANE · 89 bp · p 4.4e-06 · regional, not allelic
Overall
CADD	25.5	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 0.00667% African / African-American · 5/74,980 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00161%

Overall 0.00118% 19/1,613,660 alleles · very rare exomes 15/1,461,456 · genomes 4/152,204 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00667%	14,996
East Asian	0.00446%	22,438
Remaining individualsnot grpmax-eligible	0.0032%	31,247
European (non-Finnish)	0.000848%	117,976

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: UBAP1
Protein: p.Ala152Val
Coding: c.455C>T
MANE Select: NM_016525
Type: single nucleotide variant
Location: chr9:34241480 (GRCh38)
Gene constraint: LOEUF 0.285 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.60 · 3 PDB
Residue 152: a UniProt-annotated variant site (in spg80)

Full UBAP1 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

Similar variants

UBAP1 p.Ala152= Likely benign ★ same residue
UBAP1 p.Glu445Lys Uncertain significance ★★ ⚠ same condition
UBAP1 c.-104C>G Uncertain significance ★ same condition
UBAP1 c.-146G>T Uncertain significance ★ same condition
UBAP1 c.-167G>A Uncertain significance ★ same condition
UBAP1 c.-167G>C Uncertain significance ★ same condition
UBAP1 c.-167G>T Uncertain significance ★ same condition
UBAP1 c.-178G>A 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/ubap1-p-ala152val (accessed [today's date]).

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