Is C1QL2 p.Ile32= (c.96C>A) pathogenic?

C1QL2 p.Ile32= (c.96C>A) is classified Benign in C1QL2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). Common (popmax 5.63%, afr) — too common for a highly-penetrant pathogenic allele.

C1QL2 p.Ile32=

Q: How common is C1QL2 p.Ile32= (c.96C>A) in the general population?

C1QL2 p.Ile32= (c.96C>A) is common (popmax 5.63%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.96C>A · rs113019193 · VCV778000

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 5.63%, afr) — too common for a highly-penetrant pathogenic allele

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 4.1	GERP -1.8, phastCons 1
Overall
CADD	11.46	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.63% African / African-American · 4,009/71,236 alleles

Filtering AF 5.48% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.42%

Overall 0.344% 5,438/1,579,030 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.63%	18
Middle Eastern	1.04%	96
Admixed American	0.56%	179
Remaining individualsnot grpmax-eligible	0.508%	197
European (non-Finnish)	0.0618%	1,617
Ashkenazi Jewishnot grpmax-eligible	0.0599%	1,669
South Asian	0.0126%	7,935

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: C1QL2
Protein: p.Ile32=
Coding: c.96C>A
MANE Select: NM_182528
dbSNP: rs113019193
Type: single nucleotide variant
Location: chr2:119158174 (GRCh38)
Gene constraint: LOEUF 1.421 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.90

Full C1QL2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

C1QL2 p.Ala123Val Uncertain significance ★ ⚠ same type
C1QL2 p.Ala126Thr Uncertain significance ★ ⚠ same type
C1QL2 p.Ala16Thr Uncertain significance ★ ⚠ same type
C1QL2 p.Ala8Val Uncertain significance ★ ⚠ same type
C1QL2 p.Arg90Gln Uncertain significance ★ ⚠ same type
C1QL2 p.Arg90Gly Uncertain significance ★ ⚠ same type
C1QL2 p.Asp34Tyr Uncertain significance ★ ⚠ same type
C1QL2 p.Asp80Tyr 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/c1ql2-p-ile32 (accessed [today's date]).

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