Is UBAP1 p.Ser301Phe (c.902C>T) pathogenic?

UBAP1 p.Ser301Phe (c.902C>T) is classified Conflicting classifications of pathogenicity in UBAP1 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-06-01). AlphaMissense: likely benign (0.0901); Very rare (popmax 0.0022%, nfe); Associated with Inborn genetic diseases.

What condition is associated with UBAP1 p.Ser301Phe (c.902C>T)?

UBAP1 p.Ser301Phe (c.902C>T) is associated with Inborn genetic diseases (ClinVar).

How common is UBAP1 p.Ser301Phe (c.902C>T) in the general population?

UBAP1 p.Ser301Phe (c.902C>T) is very rare (popmax 0.0022%, nfe) (gnomAD).

What do computational predictors say about UBAP1 p.Ser301Phe (c.902C>T)?

AlphaMissense predicts likely benign (score 0.0901) — an in-silico prediction, not a clinical call.

UBAP1 p.Ser301Phe

c.902C>T · VCV3464984

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0901 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0901	likely benign
REVEL	0.045	moderately benign-leaning
SaProt	LLR -8.10	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 3.3	GERP 1.9, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 9,962 bp · p 0.0098 · regional, not allelic
Overall
CADD	19.53	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% European (non-Finnish) · 26/1,180,048 alleles

Filtering AF 0.00153% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0013%

Overall 0.00161% 26/1,614,070 alleles · very rare exomes 22/1,461,890 · genomes 4/152,180 · joint denominator

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.Ser301Phe
Coding: c.902C>T
MANE Select: NM_016525
Type: single nucleotide variant
Location: chr9:34241927 (GRCh38)
Gene constraint: LOEUF 0.285 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.60 · 3 PDB
Residue 301: a UniProt-annotated variant site (in spg80); a UniProt-annotated variant site (in spg80; uncertain significance)

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.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
UBAP1 c.-181G>T 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-ser301phe (accessed [today's date]).

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