Is CUBN p.Leu1625Phe (c.4873C>T) pathogenic?

CUBN p.Leu1625Phe (c.4873C>T) is classified Uncertain significance in CUBN (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-08-04). AlphaMissense: likely benign (0.0711); Ultra-rare (popmax 0.0935%, afr); Associated with Inborn genetic diseases.

What condition is associated with CUBN p.Leu1625Phe (c.4873C>T)?

CUBN p.Leu1625Phe (c.4873C>T) is associated with Inborn genetic diseases, Imerslund-Grasbeck syndrome, proteinuria, chronic benign (ClinVar).

How common is CUBN p.Leu1625Phe (c.4873C>T) in the general population?

CUBN p.Leu1625Phe (c.4873C>T) is ultra-rare (popmax 0.0935%, afr) (gnomAD).

What do computational predictors say about CUBN p.Leu1625Phe (c.4873C>T)?

AlphaMissense predicts likely benign (score 0.0711) — an in-silico prediction, not a clinical call.

CUBN p.Leu1625Phe

c.4873C>T · rs201801709 · VCV2224886

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0711 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0935%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0711	likely benign
REVEL	0.184	benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.83	GERP -1.2, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 84 kb · p 0.074 · regional, not allelic
Overall
CADD	15.14	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 0.0935% African / African-American · 70/74,880 alleles

Filtering AF 0.0758% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0694%

Overall 0.00484% 78/1,612,686 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0935%	1,070
Middle Eastern	0.0164%	6,084
Admixed American	0.005%	19,998
European (non-Finnish)	0.000339%	294,719

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: CUBN
Protein: p.Leu1625Phe
Coding: c.4873C>T
MANE Select: NM_001081
dbSNP: rs201801709
Type: single nucleotide variant
Location: chr10:16952372 (GRCh38)
Gene constraint: LOEUF 0.756 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1625: a disulfide bond; a UniProt-annotated variant site (in prochob); the cub 11 domain

Full CUBN 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

Also linked: Imerslund-Grasbeck syndrome proteinuria, chronic benign Imerslund-Grasbeck syndrome type 1

Similar variants

CUBN c.10033-1G>A Likely pathogenic ★★ same condition
CUBN c.1230+1G>A Pathogenic/Likely pathogenic ★★ same condition
CUBN c.3672+2T>C Likely pathogenic ★★ same condition
CUBN c.3829+1G>A Pathogenic/Likely pathogenic ★★ same condition
CUBN c.4350+2T>C Likely pathogenic ★★ same condition
CUBN c.6821+3A>G Pathogenic/Likely pathogenic ★★ same condition
CUBN c.6822-1G>A Likely pathogenic ★★ same condition
CUBN c.8598+1G>T Likely pathogenic ★★ 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/cubn-p-leu1625phe (accessed [today's date]).

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