Is BLM p.Ser1106del (c.3316_3318del) pathogenic?

BLM p.Ser1106del (c.33163318del) is classified Uncertain significance in BLM (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-22). No gnomAD frequency available for this variant; Associated with hereditary neoplastic syndrome.

What condition is associated with BLM p.Ser1106del (c.3316_3318del)?

BLM p.Ser1106del (c.3316_3318del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BLM p.Ser1106del (c.3316_3318del) in the general population?

BLM p.Ser1106del (c.3316_3318del) is no gnomAD frequency available for this variant (gnomAD).

BLM p.Ser1106del

c.3316_3318del · rs1297841892 · VCV3224433

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 0.21	GERP -2.5, phastCons 0.32

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BLM
Protein: p.Ser1106del
Coding: c.3316_3318del
MANE Select: NM_000057
dbSNP: rs1297841892
Type: Deletion
Location: chr15:90798293 (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 1106: the 'dna holliday junction binding' region

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

Similar variants

BLM p.Ser1106Cys Uncertain significance ★★ ⚠ same residue
BLM c.2193+1_2193+9del Pathogenic/Likely pathogenic ★★ same condition
BLM c.3210+2del Pathogenic/Likely pathogenic ★★ same condition
BLM c.99-8_112del Pathogenic/Likely pathogenic ★★ same condition
BLM p.Arg545fs Pathogenic/Likely pathogenic ★★ same condition
BLM p.Arg836fs Pathogenic ★★ same condition
BLM p.Asn448fs Pathogenic ★★ same condition
BLM p.Asp1010fs Pathogenic/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-ser1106del (accessed [today's date]).

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