Is BLNK p.Val9fs (c.26del) pathogenic?

BLNK p.Val9fs (c.26del) is classified Pathogenic in BLNK (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-10). Absent from gnomAD; Associated with agammaglobulinemia 4, autosomal recessive.

What condition is associated with BLNK p.Val9fs (c.26del)?

BLNK p.Val9fs (c.26del) is associated with agammaglobulinemia 4, autosomal recessive (ClinVar).

How common is BLNK p.Val9fs (c.26del) in the general population?

BLNK p.Val9fs (c.26del) is absent from gnomAD (gnomAD).

BLNK p.Val9fs

c.26del · rs2493183249 · VCV2090455

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

agammaglobulinemia 4, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 1 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.7	phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: BLNK
Protein: p.Val9fs
Coding: c.26del
MANE Select: NM_013314
dbSNP: rs2493183249
Type: Deletion
Location: chr10:96271373 (GRCh38)
Gene constraint: LOEUF 0.517 · pLI 0.90 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.46 · 1 PDB

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

Disease context

agammaglobulinemia 4, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BLNK p.Val9Ile Uncertain significance ★ ⚠ same residue
BLNK c.1096-17del Benign/Likely benign ★★ same condition
BLNK c.526-22_526-19del Likely benign ★★ same condition
BLNK p.Lys344fs Pathogenic ★ same condition
BLNK p.Val206del Uncertain significance ★ same condition
BLNK c.775-12del Benign ★ same condition
BLNK c.902+2T>C Likely pathogenic ★★ same condition
BLNK p.Ala176Val 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/blnk-p-val9fs (accessed [today's date]).

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