Is BLM p.Asp239= (c.717T>C) pathogenic?

BLM p.Asp239= (c.717T>C) is classified Likely benign in BLM (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-16). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BLM p.Asp239= (c.717T>C)?

BLM p.Asp239= (c.717T>C) is associated with hereditary neoplastic syndrome, Bloom syndrome (ClinVar).

How common is BLM p.Asp239= (c.717T>C) in the general population?

BLM p.Asp239= (c.717T>C) is absent from gnomAD v4.1 (gnomAD).

BLM p.Asp239=

c.717T>C · rs2505394569 · VCV1757536

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

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 -1.7	GERP -1.1
Overall
CADD	0.968	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: BLM
Protein: p.Asp239=
Coding: c.717T>C
MANE Select: NM_000057
dbSNP: rs2505394569
Type: single nucleotide variant
Location: chr15:90749985 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 61.10 · 16 PDB

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Bloom syndrome

Similar variants

BLM p.Asp239Ala Uncertain significance ★★ ⚠ same residue
BLM p.Asp239Asn Uncertain significance ★★ ⚠ same residue
BLM p.Asp239Gly Uncertain significance ★★ ⚠ same residue
BLM p.Asp239His Uncertain significance ★★ ⚠ same residue
BLM p.Asp239Val Uncertain significance ★★ ⚠ same residue
BLM p.Asp239Glu Uncertain significance ★ ⚠ same residue
BLM c.1087+1G>A Likely pathogenic ★★ same condition
BLM c.1088-1G>A 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/blm-p-asp239 (accessed [today's date]).

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