Is CMIP p.Arg282= (c.846A>C) pathogenic?

CMIP p.Arg282= (c.846A>C) is classified Likely benign in CMIP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-07). Very rare (popmax 0.00619%, nfe); Associated with CMIP-related disorder.

What condition is associated with CMIP p.Arg282= (c.846A>C)?

CMIP p.Arg282= (c.846A>C) is associated with CMIP-related disorder (ClinVar).

How common is CMIP p.Arg282= (c.846A>C) in the general population?

CMIP p.Arg282= (c.846A>C) is very rare (popmax 0.00619%, nfe) (gnomAD).

CMIP p.Arg282=

c.846A>C · rs754812064 · VCV3033990

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00619%, nfe)

Conditions

CMIP-related disorder

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 -0.24	GERP -4.8, phastCons 0.004
Overall
CADD	7.383	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00619% European (non-Finnish) · 73/1,178,396 alleles

Filtering AF 0.00503% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00463%

Overall 0.0046% 74/1,610,036 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00619%	16,142
Remaining individualsnot grpmax-eligible	0.0016%	62,354

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: CMIP
Protein: p.Arg282=
Coding: c.846A>C
MANE Select: NM_198390
dbSNP: rs754812064
Type: single nucleotide variant
Location: chr16:81670162 (GRCh38)
Gene constraint: LOEUF 0.189 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 79.52

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

Disease context

CMIP-related disorder

Similar variants

CMIP p.Ala92Thr Uncertain significance ★ ⚠ same condition
CMIP p.Arg149Ter Uncertain significance ★ same condition
CMIP p.Glu495Lys Uncertain significance ⚠ same condition
CMIP p.Ile199Val Uncertain significance ⚠ same condition
CMIP c.1896+8C>T Likely benign same condition
CMIP c.2091+4C>T Likely benign same condition
CMIP c.2091+5G>A Benign same condition
CMIP p.Arg253= 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/cmip-p-arg282 (accessed [today's date]).

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