Is CORO7 p.Val322Ile (c.964G>A) pathogenic?

CORO7 p.Val322Ile (c.964G>A) is classified Uncertain significance in CORO7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-21). AlphaMissense: likely benign (0.0982); Ultra-rare (popmax 0.0164%, mid).

How common is CORO7 p.Val322Ile (c.964G>A) in the general population?

CORO7 p.Val322Ile (c.964G>A) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about CORO7 p.Val322Ile (c.964G>A)?

AlphaMissense predicts likely benign (score 0.0982) — an in-silico prediction, not a clinical call.

CORO7 p.Val322Ile

c.964G>A · rs765091340 · VCV2568435

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0982 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0982	likely benign
REVEL	0.175	moderately benign-leaning
SaProt	LLR -9.97	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 2.2	GERP 0.71, phastCons 0.98
Regional constraint	o/e 1.05	unconstrained · MANE · 61 kb · p 0.1 · regional, not allelic
Overall
CADD	20.5	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 0.0164% Middle Eastern · 1/6,080 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.00248% 40/1,611,836 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,080
East Asian	0.00891%	11,220
African / African-American	0.00534%	18,724
European (non-Finnish)	0.00263%	38,058

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: CORO7
Protein: p.Val322Ile
Coding: c.964G>A
MANE Select: NM_024535
dbSNP: rs765091340
Type: single nucleotide variant
Location: chr16:4364855 (GRCh38)
Gene constraint: LOEUF 1.089 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.71 · 1 PDB

Full CORO7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CORO7-PAM16 p.Arg193Gln Benign ★★ ⚠ same type
CORO7 p.Arg601His Uncertain significance ★ ⚠ same type
CORO7 p.Asp50Asn Uncertain significance ★ ⚠ same type
CORO7 p.Lys151Thr Uncertain significance ★ ⚠ same type
CORO7-PAM16 p.Ala403Val Uncertain significance ★ ⚠ same type
CORO7-PAM16 p.Arg559Cys Uncertain significance ★ ⚠ same type
CORO7-PAM16 p.Arg876Trp Uncertain significance ★ ⚠ same type
CORO7-PAM16 p.Cys691Tyr 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/coro7-p-val322ile (accessed [today's date]).

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