Is BLK p.Lys13= (c.39G>A) pathogenic?

BLK p.Lys13= (c.39G>A) is classified Benign/Likely benign in BLK (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-11-15). Rare (popmax 0.753%, afr); Associated with systemic lupus erythematosus.

What condition is associated with BLK p.Lys13= (c.39G>A)?

BLK p.Lys13= (c.39G>A) is associated with systemic lupus erythematosus, maturity-onset diabetes of the young type 11 (ClinVar).

How common is BLK p.Lys13= (c.39G>A) in the general population?

BLK p.Lys13= (c.39G>A) is rare (popmax 0.753%, afr) (gnomAD).

How is Systemic lupus erythematosus inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

BLK p.Lys13=

c.39G>A · rs142129056 · VCV258177

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.753%, afr)

Conditions

systemic lupus erythematosus

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 0.64	GERP 0.68, phastCons 0.46
Overall
CADD	1.717	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.753% African / African-American · 565/75,008 alleles

Filtering AF 0.702% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.681%

Overall 0.0374% 603/1,614,026 alleles · rare exomes 287/1,461,780 · genomes 316/152,246 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.753%	133
Admixed American	0.03%	3,335
Remaining individualsnot grpmax-eligible	0.0256%	3,906
Middle Eastern	0.0165%	6,062
European (non-Finnish)	0.000254%	393,346

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: BLK
Protein: p.Lys13=
Coding: c.39G>A
MANE Select: NM_001715
dbSNP: rs142129056
Type: single nucleotide variant
Location: chr8:11543263 (GRCh38)
Gene constraint: LOEUF 1.295 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.89
Residue 13: the 'disordered' region

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

Disease context

systemic lupus erythematosus — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: maturity-onset diabetes of the young type 11

For Systemic lupus erythematosus (Orphanet):

Inheritance: Not applicable
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-5 / 10 000 (France)

Similar variants

BLK p.Arg131Gln Uncertain significance ★★ ⚠ same condition
BLK p.Arg180His Uncertain significance ★★ ⚠ same condition
BLK p.Arg295Trp Uncertain significance ★★ same condition
BLK p.Arg298Gln Uncertain significance ★★ ⚠ same condition
BLK p.Gln226Pro Uncertain significance ★★ ⚠ same condition
BLK p.Gly451Ser Uncertain significance ★★ ⚠ same condition
BLK p.His55Arg Uncertain significance ★★ ⚠ same condition
BLK p.Ile338Thr 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/blk-p-lys13 (accessed [today's date]).

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