Is UNC79 p.Pro1278Ser (c.3832C>T) pathogenic?

UNC79 p.Pro1278Ser (c.3832C>T) is classified Uncertain significance in UNC79 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-24). Very rare (popmax 0.00134%, afr); Associated with UNC79-related disorder.

What condition is associated with UNC79 p.Pro1278Ser (c.3832C>T)?

UNC79 p.Pro1278Ser (c.3832C>T) is associated with UNC79-related disorder (ClinVar).

How common is UNC79 p.Pro1278Ser (c.3832C>T) in the general population?

UNC79 p.Pro1278Ser (c.3832C>T) is very rare (popmax 0.00134%, afr) (gnomAD).

UNC79 p.Pro1278Ser

c.3832C>T · rs2066405972 · VCV2636036

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Conditions

UNC79-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.178	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.7, phastCons 1
Overall
CADD	23.5	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,902 alleles

Overall 6.2e-05% 1/1,613,400 alleles · very rare exomes 0/1,461,258 · genomes 1/152,142 · 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.Pro1278Ser
Coding: c.3832C>T
MANE Select: NM_001395159
dbSNP: rs2066405972
Type: single nucleotide variant
Location: chr14:93612808 (GRCh38)
Gene constraint: LOEUF 0.168 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.95 · 3 PDB
Residue 1278: an α-helix

Full UNC79 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

UNC79-related disorder

Similar variants

UNC79 p.Ile1680Thr Uncertain significance ★★ same condition
UNC79 p.Trp255Ter Pathogenic ★ same condition
UNC79 p.Arg1332Ter Conflicting classifications of pathogenicity ★ ⚠ same condition
UNC79 p.Arg747Ter Uncertain significance ★ same condition
UNC79 p.Gln2472Ter Uncertain significance ★ same condition
UNC79 p.Ile505Val Uncertain significance ★ same condition
UNC79 c.1052+2T>A Uncertain significance same condition
UNC79 p.Glu2370Gly 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-pro1278ser (accessed [today's date]).

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