Is CCDC82 p.Ile34Val (c.100A>G) pathogenic?

CCDC82 p.Ile34Val (c.100A>G) is classified Likely benign in CCDC82 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-01). AlphaMissense: likely benign (0.0793); Rare (popmax 0.992%, nfe).

How common is CCDC82 p.Ile34Val (c.100A>G) in the general population?

CCDC82 p.Ile34Val (c.100A>G) is rare (popmax 0.992%, nfe) (gnomAD).

What do computational predictors say about CCDC82 p.Ile34Val (c.100A>G)?

AlphaMissense predicts likely benign (score 0.0793) — an in-silico prediction, not a clinical call.

CCDC82 p.Ile34Val

c.100A>G · rs61746142 · VCV2642308

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0793 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.992%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0793	likely benign
REVEL	0.01	strongly benign-leaning
SaProt	LLR -5.97	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.2	GERP -3.2
Regional constraint	o/e 0.93	unconstrained · MANE · 31 kb · p 0.074 · regional, not allelic
Overall
CADD	1.832	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.992% European (non-Finnish) · 11,697/1,179,626 alleles

Filtering AF 0.976% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.97%

Overall 0.814% 13,135/1,613,526 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.992%	101
Remaining individualsnot grpmax-eligible	0.659%	152
South Asian	0.453%	221
Finnishnot grpmax-eligible	0.425%	235
Admixed American	0.338%	295
African / African-American	0.164%	610
Middle Eastern	0.116%	865
Ashkenazi Jewishnot grpmax-eligible	0.0237%	4,224
East Asian	0.00446%	22,428

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: CCDC82
Protein: p.Ile34Val
Coding: c.100A>G
MANE Select: NM_024725
dbSNP: rs61746142
Type: single nucleotide variant
Location: chr11:96384648 (GRCh38)
Gene constraint: LOEUF 1.06 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.94
Residue 34: the 'disordered' region

Full CCDC82 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC82 p.Thr108Ala Benign ★★ same type
CCDC82 p.Arg23Ter Likely pathogenic ★ same type
CCDC82 p.Ala233Thr Uncertain significance ★ ⚠ same type
CCDC82 p.Ala351Thr Uncertain significance ★ ⚠ same type
CCDC82 p.Arg11Gly Uncertain significance ★ ⚠ same type
CCDC82 p.Arg179Gln Uncertain significance ★ ⚠ same type
CCDC82 p.Arg179Ter Conflicting classifications of pathogenicity ★ same type
CCDC82 p.Arg211Cys 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/ccdc82-p-ile34val (accessed [today's date]).

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