Is UNC79 p.Pro889Leu (c.2666C>T) pathogenic?

UNC79 p.Pro889Leu (c.2666C>T) is classified Uncertain significance in UNC79 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-30). Very rare (popmax 0.00446%, eas); Associated with Inborn genetic diseases.

What condition is associated with UNC79 p.Pro889Leu (c.2666C>T)?

UNC79 p.Pro889Leu (c.2666C>T) is associated with Inborn genetic diseases (ClinVar).

How common is UNC79 p.Pro889Leu (c.2666C>T) in the general population?

UNC79 p.Pro889Leu (c.2666C>T) is very rare (popmax 0.00446%, eas) (gnomAD).

UNC79 p.Pro889Leu

c.2666C>T · rs746598956 · VCV2351545

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.26	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.3, phastCons 1
Overall
CADD	24.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,858 alleles

Filtering AF 0.000739% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000277%

Overall 0.000124% 2/1,614,076 alleles · very rare exomes 2/1,461,852 · genomes 0/152,224 · 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: UNC79
Protein: p.Pro889Leu
Coding: c.2666C>T
MANE Select: NM_001395159
dbSNP: rs746598956
Type: single nucleotide variant
Location: chr14:93582207 (GRCh38)
Gene constraint: LOEUF 0.168 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.95 · 3 PDB

Full UNC79 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

UNC79 p.Pro2467Arg Uncertain significance ★★ same condition
UNC79 p.Thr2409Met Uncertain significance ★★ same condition
UNC79 p.Tyr539Phe Uncertain significance ★★ same condition
UNC79 c.6134-1G>A Likely pathogenic ★ same condition
UNC79 p.Gln1343Ter Pathogenic ★ same condition
UNC79 p.Lys251Ter Pathogenic ★ same condition
UNC79 p.Ala1041Thr Uncertain significance ★ same condition
UNC79 p.Ala1063Ser 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/unc79-p-pro889leu (accessed [today's date]).

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