Is BARHL2 p.Pro34= (c.102G>A) pathogenic?

BARHL2 p.Pro34= (c.102G>A) is classified Likely benign in BARHL2 (ClinVar, No assertion criteria, 1 submitter). Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with BARHL2 p.Pro34= (c.102G>A)?

BARHL2 p.Pro34= (c.102G>A) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is BARHL2 p.Pro34= (c.102G>A) in the general population?

BARHL2 p.Pro34= (c.102G>A) is absent from gnomAD v4.1 (gnomAD).

BARHL2 p.Pro34=

c.102G>A · rs2100643855 · VCV2681497

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.1	GERP -2.2, phastCons 0.001
Overall
CADD	8.443	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BARHL2
Protein: p.Pro34=
Coding: c.102G>A
MANE Select: NM_020063
dbSNP: rs2100643855
Type: single nucleotide variant
Location: chr1:90717094 (GRCh38)
Gene constraint: LOEUF 0.629 · pLI 0.62 (gnomAD)
Structure: AlphaFold pLDDT 62.10 · 11 PDB
Residue 34: the 'disordered' region

Full BARHL2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

BARHL2 p.Ala131Ser Uncertain significance ★ ⚠ same type
BARHL2 p.Ala332Val Uncertain significance ★ ⚠ same type
BARHL2 p.Ala334Thr Uncertain significance ★ ⚠ same type
BARHL2 p.Ala47Val Uncertain significance ★ ⚠ same type
BARHL2 p.Ala99Val Uncertain significance ★ ⚠ same type
BARHL2 p.Arg216Gln Uncertain significance ★ ⚠ same type
BARHL2 p.Arg216Trp Uncertain significance ★ ⚠ same type
BARHL2 p.Arg354Trp Uncertain significance ★ ⚠ same type

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/barhl2-p-pro34 (accessed [today's date]).

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