Is CORO2B p.Met126Val (c.376A>G) pathogenic?

CORO2B p.Met126Val (c.376A>G) is classified Uncertain significance in CORO2B (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-10). AlphaMissense: likely benign (0.1218); Ultra-rare (popmax 0.0111%, sas).

How common is CORO2B p.Met126Val (c.376A>G) in the general population?

CORO2B p.Met126Val (c.376A>G) is ultra-rare (popmax 0.0111%, sas) (gnomAD).

What do computational predictors say about CORO2B p.Met126Val (c.376A>G)?

AlphaMissense predicts likely benign (score 0.1218) — an in-silico prediction, not a clinical call.

CORO2B p.Met126Val

c.376A>G · VCV4655931

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1218 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0111%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1218	likely benign
REVEL	0.189	benign-leaning
SaProt	LLR -9.41	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 7.9	GERP 0.84, phastCons 1
Regional constraint	o/e 0.65	unconstrained · MANE · 140 kb · p 2.5e-16 · regional, not allelic
Overall
CADD	22.6	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 0.0111% South Asian · 10/90,434 alleles

Filtering AF 0.00598% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00456%

Overall 0.00254% 41/1,612,160 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0111%	9,043
European (non-Finnish)	0.00246%	40,666
Remaining individualsnot grpmax-eligible	0.0016%	62,420
African / African-American	0.00133%	74,912

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: CORO2B
Protein: p.Met126Val
Coding: c.376A>G
MANE Select: NM_006091
Type: single nucleotide variant
Location: chr15:68710774 (GRCh38)
Gene constraint: LOEUF 0.633 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 91.58

Full CORO2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CORO2B p.Ala334Val Uncertain significance ★ ⚠ same type
CORO2B p.Ala60Thr Uncertain significance ★ ⚠ same type
CORO2B p.Arg124Gln Uncertain significance ★ ⚠ same type
CORO2B p.Arg13His Uncertain significance ★ ⚠ same type
CORO2B p.Arg213His Uncertain significance ★ ⚠ same type
CORO2B p.Arg227Gln Uncertain significance ★ ⚠ same type
CORO2B p.Arg236Gln Uncertain significance ★ ⚠ same type
CORO2B p.Arg244Thr 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/coro2b-p-met126val (accessed [today's date]).

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