Is C1QB p.Thr30= (c.90C>T) pathogenic?

C1QB p.Thr30= (c.90C>T) is classified Likely benign in C1QB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-26). Very rare (popmax 0.00364%, nfe).

How common is C1QB p.Thr30= (c.90C>T) in the general population?

C1QB p.Thr30= (c.90C>T) is very rare (popmax 0.00364%, nfe) (gnomAD).

C1QB p.Thr30=

c.90C>T · rs748217347 · VCV1641570

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00364%, nfe)

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 -13	GERP -2.7
Overall
CADD	0.113	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00364% European (non-Finnish) · 43/1,179,968 alleles

Filtering AF 0.00275% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00244%

Overall 0.00291% 47/1,613,916 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00364%	27,441
Remaining individualsnot grpmax-eligible	0.0032%	31,238
African / African-American	0.00267%	37,445

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: C1QB
Protein: p.Thr30=
Coding: c.90C>T
MANE Select: NM_001378156
dbSNP: rs748217347
Type: single nucleotide variant
Location: chr1:22659552 (GRCh38)
Gene constraint: LOEUF 1.001 · pLI 0.25 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 79.87 · 11 PDB

Full C1QB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

C1QB p.Thr30Ser Uncertain significance ★ ⚠ same residue
C1QB p.Arg175Ter Likely pathogenic ★★ same type
C1QB p.Ala121Thr Uncertain significance ★★ ⚠ same type
C1QB p.Ala124Asp Uncertain significance ★★ ⚠ same type
C1QB p.Arg134Gln Uncertain significance ★★ ⚠ same type
C1QB p.Arg134Trp Uncertain significance ★★ ⚠ same type
C1QB p.Arg186Gln Uncertain significance ★★ ⚠ same type
C1QB p.Asp21Asn Uncertain significance ★★ ⚠ same type

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/c1qb-p-thr30 (accessed [today's date]).

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