Is CRB2 p.Phe882Val (c.2644T>G) pathogenic?

CRB2 p.Phe882Val (c.2644T>G) is classified Uncertain significance in CRB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-16). AlphaMissense: likely pathogenic (0.6941); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CRB2 p.Phe882Val (c.2644T>G)?

CRB2 p.Phe882Val (c.2644T>G) is associated with Inborn genetic diseases (ClinVar).

How common is CRB2 p.Phe882Val (c.2644T>G) in the general population?

CRB2 p.Phe882Val (c.2644T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CRB2 p.Phe882Val (c.2644T>G)?

AlphaMissense predicts likely pathogenic (score 0.6941) — an in-silico prediction, not a clinical call.

CRB2 p.Phe882Val

c.2644T>G · rs2550687680 · VCV2405164

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6941 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,514,884)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6941	likely pathogenic
REVEL	0.285	benign-leaning
SaProt	LLR -8.04	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 21 kb · p 0.85 · regional, not allelic
Overall
CADD	24.6	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

No allele count reported in gnomAD v4.1 (AN 1,514,884). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CRB2
Protein: p.Phe882Val
Coding: c.2644T>G
MANE Select: NM_173689
dbSNP: rs2550687680
Type: single nucleotide variant
Location: chr9:123373175 (GRCh38)
Gene constraint: LOEUF 1.202 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.95 · 1 PDB
Residue 882: a UniProt-annotated variant site (in vmckd; uncertain significance); the laminin g-like 3 domain; a UniProt-annotated variant site (in fsgs9; uncertain significance)

Full CRB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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CRB2 p.Ala228Thr Uncertain significance ★★ ⚠ same condition
CRB2 p.Ala26Asp Uncertain significance ★★ ⚠ same condition
CRB2 p.Ala325Val Uncertain significance ★★ ⚠ same condition
CRB2 p.Ala80Thr Uncertain significance ★★ ⚠ same condition
CRB2 p.Ala887Thr Uncertain significance ★★ ⚠ same condition
CRB2 p.Ala914Val Uncertain significance ★★ ⚠ 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/crb2-p-phe882val (accessed [today's date]).

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