Is CMIP p.Val404Met (c.1210G>A) pathogenic?

CMIP p.Val404Met (c.1210G>A) is classified Uncertain significance in CMIP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-25). AlphaMissense: likely benign (0.1964); Very rare (popmax 0.00356%, amr).

How common is CMIP p.Val404Met (c.1210G>A) in the general population?

CMIP p.Val404Met (c.1210G>A) is very rare (popmax 0.00356%, amr) (gnomAD).

What do computational predictors say about CMIP p.Val404Met (c.1210G>A)?

AlphaMissense predicts likely benign (score 0.1964) — an in-silico prediction, not a clinical call.

CMIP p.Val404Met

c.1210G>A · VCV3494111

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1964 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00356%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1964	likely benign
REVEL	0.26	benign-leaning
SaProt	LLR -7.50	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 12	GERP 2.2, phastCons 1
Regional constraint	o/e 1.20	unconstrained · MANE · 13 kb · p 0.01 · regional, not allelic
Overall
CADD	28.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00356% Admixed American · 2/56,250 alleles

Filtering AF 0.000907% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000451%

Overall 0.000487% 7/1,438,326 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00356%	28,125
South Asian	0.00341%	29,293
European (non-Finnish)	0.000171%	584,754

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.Val404Met
Coding: c.1210G>A
MANE Select: NM_198390
Type: single nucleotide variant
Location: chr16:81678450 (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

Similar variants

CMIP p.Val404Glu Uncertain significance ★ ⚠ same residue
CMIP c.1638+10G>A Likely benign ★★ same type
CMIP c.2269-10C>T Benign/Likely benign ★★ same type
CMIP p.Asn295= Benign ★★ same type
CMIP p.Leu369= Likely benign ★★ same type
CMIP p.Pro414= Benign ★★ same type
CMIP p.Val547= Benign ★★ same type
CMIP c.1035-1G>A 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/cmip-p-val404met (accessed [today's date]).

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