Is CIDEC p.Leu11= (c.33C>G) pathogenic?

CIDEC p.Leu11= (c.33C>G) is classified Benign in CIDEC (ClinVar, Multiple submitters, 5 submitters; last evaluated 2022-05-05). Common (popmax 16.2%, sas) — too common for a highly-penetrant pathogenic allele.

CIDEC p.Leu11=

Q: How common is CIDEC p.Leu11= (c.33C>G) in the general population?

CIDEC p.Leu11= (c.33C>G) is common (popmax 16.2%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.33C>G · rs17851444 · VCV128772

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 16.2%, sas) — 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 0.53	GERP -2.6, phastCons 0.99
Overall
CADD	6.312	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 16.2% South Asian · 14,722/91,058 alleles

Filtering AF 15.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 15.9%

Overall 11.7% 189,343/1,612,418 alleles · common

Ancestry group	Frequency	1 in
South Asiangrpmax	16.2%	6
Middle Eastern	12.9%	8
European (non-Finnish)	12.4%	8
Ashkenazi Jewishnot grpmax-eligible	12.3%	8
Remaining individualsnot grpmax-eligible	11.5%	9
Finnishnot grpmax-eligible	10.5%	9
Amishnot grpmax-eligible	7.35%	14
Admixed American	5.94%	17
African / African-American	5.35%	19
East Asian	4.62%	22

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: CIDEC
Protein: p.Leu11=
Coding: c.33C>G
MANE Select: NM_001321142
dbSNP: rs17851444
Type: single nucleotide variant
Location: chr3:9878454 (GRCh38)
Gene constraint: LOEUF 0.927 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.19
Residue 11: the 'required for liquid-liquid phase separation (llps)' region

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

Similar variants

CIDEC p.Arg182His Uncertain significance ★★ ⚠ same type
CIDEC p.Ile156Thr Uncertain significance ★★ ⚠ same type
CIDEC p.Met195Ile Uncertain significance ★★ ⚠ same type
CIDEC p.Val54Met Uncertain significance ★★ ⚠ same type
CIDEC c.207+180G>A Benign ★★ same type
CIDEC c.208-91C>T Benign ★★ same type
CIDEC c.53+77T>A Benign ★★ same type
CIDEC c.-25-52G>T Benign ★★ 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/cidec-p-leu11 (accessed [today's date]).

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