Is SON p.Pro624Arg (c.1871C>G) pathogenic?

SON p.Pro624Arg (c.1871C>G) is classified Uncertain significance in SON (ClinVar, Single submitter, 1 submitter; last evaluated 2020-11-13). AlphaMissense: likely pathogenic (0.6535); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SON p.Pro624Arg (c.1871C>G)?

SON p.Pro624Arg (c.1871C>G) is associated with Inborn genetic diseases (ClinVar).

How common is SON p.Pro624Arg (c.1871C>G) in the general population?

SON p.Pro624Arg (c.1871C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SON p.Pro624Arg (c.1871C>G)?

AlphaMissense predicts likely pathogenic (score 0.6535) — an in-silico prediction, not a clinical call.

SON p.Pro624Arg

c.1871C>G · rs2517358239 · VCV2228224

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6535 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6535	likely pathogenic
REVEL	0.175	moderately benign-leaning
SaProt	LLR -12.32	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 4.5, phastCons 1
Regional constraint	o/e 0.38	unconstrained · MANE · 83 bp · p 0.00042 · regional, not allelic
Overall
CADD	27.7	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

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: SON
Protein: p.Pro624Arg
Coding: c.1871C>G
MANE Select: NM_138927
dbSNP: rs2517358239
Type: single nucleotide variant
Location: chr21:33551102 (GRCh38)
Gene constraint: LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 36.48 · 4 PDB

Full SON 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

SON p.Pro624= Likely benign ★ same residue
SON p.Arg1112Ter Pathogenic ★★ same condition
SON p.Arg1031Cys Uncertain significance ★★ ⚠ same condition
SON p.Arg1993Cys Uncertain significance ★★ ⚠ same condition
SON p.Gly47Asp Uncertain significance ★★ ⚠ same condition
SON p.Ser1437Cys Uncertain significance ★★ ⚠ same condition
SON p.Thr1156Lys Uncertain significance ★★ ⚠ same condition
SON p.Ala1109Val Likely 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/son-p-pro624arg (accessed [today's date]).

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