Is CRCP p.Asn41Lys (c.123C>G) pathogenic?

CRCP p.Asn41Lys (c.123C>G) is classified Uncertain significance in CRCP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-12). AlphaMissense: likely pathogenic (0.9239); Absent from gnomAD v4.1.

How common is CRCP p.Asn41Lys (c.123C>G) in the general population?

CRCP p.Asn41Lys (c.123C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CRCP p.Asn41Lys (c.123C>G)?

AlphaMissense predicts likely pathogenic (score 0.9239) — an in-silico prediction, not a clinical call.

CRCP p.Asn41Lys

c.123C>G · rs1787778670 · VCV2254740

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9239 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9239	likely pathogenic
REVEL	0.37	indeterminate
SaProt	LLR -12.56	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.28	GERP 3.9, phastCons 0.11
Regional constraint	o/e 0.74	unconstrained · MANE · 37 kb · p 0.00048 · regional, not allelic
Overall
CADD	22.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CRCP
Protein: p.Asn41Lys
Coding: c.123C>G
MANE Select: NM_014478
dbSNP: rs1787778670
Type: single nucleotide variant
Location: chr7:66130821 (GRCh38)
Gene constraint: LOEUF 1.397 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.31 · 29 PDB
Residue 41: an α-helix

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

Similar variants

CRCP p.Glu144Lys Uncertain significance ★★ ⚠ same type
CRCP p.Ala72Thr Uncertain significance ★ ⚠ same type
CRCP p.Ala9Val Uncertain significance ★ ⚠ same type
CRCP p.Arg27Cys Uncertain significance ★ ⚠ same type
CRCP p.Arg59Gly Uncertain significance ★ ⚠ same type
CRCP p.Arg90Gln Uncertain significance ★ ⚠ same type
CRCP p.Arg90Trp Uncertain significance ★ ⚠ same type
CRCP p.Asn135His 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/crcp-p-asn41lys (accessed [today's date]).

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