Is BLM p.Glu880Gln (c.2638G>C) pathogenic?

BLM p.Glu880Gln (c.2638G>C) is classified Conflicting classifications of pathogenicity in BLM (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-01-27). AlphaMissense: likely benign (0.1071); Ultra-rare (popmax 0.042%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with BLM p.Glu880Gln (c.2638G>C)?

BLM p.Glu880Gln (c.2638G>C) is associated with hereditary neoplastic syndrome, Bloom syndrome (ClinVar).

How common is BLM p.Glu880Gln (c.2638G>C) in the general population?

BLM p.Glu880Gln (c.2638G>C) is ultra-rare (popmax 0.042%, nfe) (gnomAD).

What do computational predictors say about BLM p.Glu880Gln (c.2638G>C)?

AlphaMissense predicts likely benign (score 0.1071) — an in-silico prediction, not a clinical call.

BLM p.Glu880Gln

c.2638G>C · rs201770808 · VCV127489

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.1071 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.042%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1071	likely benign
REVEL	0.051	moderately benign-leaning
SaProt	LLR -6.54	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.7	GERP 2.6, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 46 kb · p 0.035 · regional, not allelic
Overall
CADD	22.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.042% European (non-Finnish) · 495/1,178,816 alleles

Filtering AF 0.0389% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0377%

Overall 0.0313% 504/1,612,700 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.042%	2,381
Remaining individualsnot grpmax-eligible	0.0128%	7,804
Finnishnot grpmax-eligible	0.00156%	64,018

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: BLM
Protein: p.Glu880Gln
Coding: c.2638G>C
MANE Select: NM_000057
dbSNP: rs201770808
Type: single nucleotide variant
Location: chr15:90782904 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 61.10 · 16 PDB
Residue 880: an α-helix; the helicase c-terminal domain

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.Glu880Gly Uncertain significance ★★ ⚠ same residue
BLM p.Glu880= Likely benign ★★ same residue
BLM c.1087+1G>A Likely pathogenic ★★ same condition
BLM c.1088-1G>A Likely pathogenic ★★ same condition
BLM c.1220+2T>C Likely pathogenic ★★ same condition
BLM c.1220+2T>G Likely pathogenic ★★ same condition
BLM c.1882+2T>C Likely pathogenic ★★ same condition
BLM c.2074+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/blm-p-glu880gln (accessed [today's date]).

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