Is C1QA p.Arg27Ter (c.79C>T) pathogenic?

C1QA p.Arg27Ter (c.79C>T) is classified Pathogenic/Likely pathogenic in C1QA (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-08-10). Very rare (popmax 0.0011%, sas); Associated with C1QA-related disorders.

What condition is associated with C1QA p.Arg27Ter (c.79C>T)?

C1QA p.Arg27Ter (c.79C>T) is associated with C1QA-related disorders, C1Q deficiency (ClinVar).

How common is C1QA p.Arg27Ter (c.79C>T) in the general population?

C1QA p.Arg27Ter (c.79C>T) is very rare (popmax 0.0011%, sas) (gnomAD).

C1QA p.Arg27Ter

c.79C>T · rs952339666 · VCV1332787

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

C1QA-related disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 3
REVEL	0.043	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP 1.5, phastCons 0.61
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/90,994 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000558% 9/1,613,806 alleles · very rare exomes 9/1,461,596 · genomes 0/152,210 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	90,994
European (non-Finnish)	0.000678%	147,491

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: C1QA
Protein: p.Arg27Ter
Coding: c.79C>T
MANE Select: NM_015991
dbSNP: rs952339666
Type: single nucleotide variant
Location: chr1:22637695 (GRCh38)
Gene constraint: LOEUF 0.997 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 83.68 · 11 PDB
Residue 27: the 'disordered' region

Full C1QA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

C1QA-related disorders

Also linked: C1Q deficiency

Similar variants

C1QA p.Arg27Gln Uncertain significance ★★ ⚠ same residue
C1QA p.Arg27Gly Uncertain significance ★ ⚠ same residue
C1QA p.Gln208Ter Pathogenic ★★ same condition
C1QA p.Gly157Asp Likely pathogenic ★★ same condition
C1QA p.Pro4Arg Uncertain significance ★★ ⚠ same condition
C1QA p.Pro54= Uncertain significance ★★ same condition
C1QA p.Glu23Lys Benign/Likely benign ★★ same condition
C1QA p.Gly92= Benign/Likely benign ★★ 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/c1qa-p-arg27ter (accessed [today's date]).

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