Is CPSF1 p.Asp801Tyr (c.2401G>T) pathogenic?

CPSF1 p.Asp801Tyr (c.2401G>T) is classified Uncertain significance in CPSF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-12). AlphaMissense: likely pathogenic (0.7083); Absent from gnomAD v4.1; Associated with myopia 27.

What condition is associated with CPSF1 p.Asp801Tyr (c.2401G>T)?

CPSF1 p.Asp801Tyr (c.2401G>T) is associated with myopia 27 (ClinVar).

How common is CPSF1 p.Asp801Tyr (c.2401G>T) in the general population?

CPSF1 p.Asp801Tyr (c.2401G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CPSF1 p.Asp801Tyr (c.2401G>T)?

AlphaMissense predicts likely pathogenic (score 0.7083) — an in-silico prediction, not a clinical call.

CPSF1 p.Asp801Tyr

c.2401G>T · VCV3779166

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7083 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,572,136)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

myopia 27

Computational evidence

Protein change
AlphaMissense	0.7083	likely pathogenic
REVEL	0.438	indeterminate
SaProt	LLR -8.14	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 1.8, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 2,917 bp · p 0.99 · regional, not allelic
Overall
CADD	26.1	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

No allele count reported in gnomAD v4.1 (AN 1,572,136). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CPSF1
Protein: p.Asp801Tyr
Coding: c.2401G>T
MANE Select: NM_013291
Type: single nucleotide variant
Location: chr8:144397398 (GRCh38)
Gene constraint: LOEUF 0.74 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.97 · 13 PDB
Residue 801: a UniProt-annotated variant site (in myp27); a turn

Full CPSF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

myopia 27 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CPSF1 p.Thr561Ile Uncertain significance ★★ ⚠ same condition
CPSF1 c.539+1G>A Likely pathogenic ★ same condition
CPSF1 c.1119+5G>T Uncertain significance ★ same condition
CPSF1 c.1120-5C>T Uncertain significance ★ same condition
CPSF1 c.1752+4A>T Uncertain significance ★ same condition
CPSF1 c.3096+5G>A Uncertain significance ★ same condition
CPSF1 c.3415-13C>G Uncertain significance ★ same condition
CPSF1 p.Gly1318Ala 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/cpsf1-p-asp801tyr (accessed [today's date]).

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