Is IL12B p.Val79= (c.237C>T) pathogenic?

IL12B p.Val79= (c.237C>T) is classified Likely benign in IL12B (ClinVar, Single submitter, 1 submitter; last evaluated 2020-07-30). Absent from gnomAD v4.1; Associated with Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency.

How common is IL12B p.Val79= (c.237C>T) in the general population?

IL12B p.Val79= (c.237C>T) is absent from gnomAD v4.1 (gnomAD).

IL12B p.Val79=

Q: What condition is associated with IL12B p.Val79= (c.237C>T)?

IL12B p.Val79= (c.237C>T) is associated with Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency (ClinVar).

Q: How is Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.237C>T · rs2113030182 · VCV1148381

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency

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 4.8	GERP 1, phastCons 1
Overall
CADD	8.177	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: IL12B
Protein: p.Val79=
Coding: c.237C>T
MANE Select: NM_002187
dbSNP: rs2113030182
Type: single nucleotide variant
Location: chr5:159323181 (GRCh38)
Gene constraint: LOEUF 0.999 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.12 · 20 PDB
Residue 79: the ig-like c2-type domain; a β-strand

Full IL12B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

IL12B p.Tyr220Ter Pathogenic/Likely pathogenic ★★ same condition
IL12B p.Arg139Cys Uncertain significance ★★ ⚠ same condition
IL12B p.Arg179Thr Uncertain significance ★★ ⚠ same condition
IL12B p.Arg288Gly Uncertain significance ★★ ⚠ same condition
IL12B p.Arg313Cys Uncertain significance ★★ ⚠ same condition
IL12B p.Arg313His Uncertain significance ★★ ⚠ same condition
IL12B p.Arg313Leu Uncertain significance ★★ ⚠ same condition
IL12B p.Asp287Val 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/il12b-p-val79 (accessed [today's date]).

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