Is SHOC2 p.Pro19Arg (c.56C>G) pathogenic?

SHOC2 p.Pro19Arg (c.56C>G) is classified Uncertain significance in SHOC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). AlphaMissense: likely benign (0.113); Very rare (popmax 0.00223%, eas); Associated with Noonan syndrome-like disorder with loose anagen hair 1.

What condition is associated with SHOC2 p.Pro19Arg (c.56C>G)?

SHOC2 p.Pro19Arg (c.56C>G) is associated with Noonan syndrome-like disorder with loose anagen hair 1 (ClinVar).

How common is SHOC2 p.Pro19Arg (c.56C>G) in the general population?

SHOC2 p.Pro19Arg (c.56C>G) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about SHOC2 p.Pro19Arg (c.56C>G)?

AlphaMissense predicts likely benign (score 0.113) — an in-silico prediction, not a clinical call.

SHOC2 p.Pro19Arg

c.56C>G · rs1847632082 · VCV877714

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.113 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Noonan syndrome-like disorder with loose anagen hair 1

Computational evidence

Protein change
AlphaMissense	0.113	likely benign
REVEL	0.084	moderately benign-leaning
SaProt	LLR -5.30	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 7.7	GERP 1.7, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 376 bp · p 0.042 · regional, not allelic
Overall
CADD	22.9	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 0.00223% East Asian · 1/44,882 alleles

Overall 6.2e-05% 1/1,612,910 alleles · very rare exomes 1/1,460,730 · genomes 0/152,180 · joint denominator

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: SHOC2
Protein: p.Pro19Arg
Coding: c.56C>G
MANE Select: NM_007373
dbSNP: rs1847632082
Type: single nucleotide variant
Location: chr10:110964414 (GRCh38)
Gene constraint: LOEUF 0.201 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.00 · 13 PDB
Residue 19: the 'disordered' region

Full SHOC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Noonan syndrome-like disorder with loose anagen hair 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SHOC2 p.Pro19Leu Uncertain significance ★ ⚠ same residue
SHOC2 p.Met173Ile Pathogenic ★★★ ⚠ same condition
SHOC2 p.Ser2Gly Pathogenic ★★★ ⚠ same condition
SHOC2 c.-1C>T Uncertain significance ★★★ same condition
SHOC2 c.1423-7C>T Benign ★★★ same condition
SHOC2 p.Glu13Ala Likely benign ★★★ same condition
SHOC2 p.Leu153= Benign ★★★ same condition
SHOC2 p.Ser4Arg Benign ★★★ 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/shoc2-p-pro19arg (accessed [today's date]).

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