Is SON p.Arg1972Cys (c.5914C>T) pathogenic?

SON p.Arg1972Cys (c.5914C>T) is classified Uncertain significance in SON (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-29). AlphaMissense: likely pathogenic (0.9434); Very rare (popmax 0.00226%, amr).

How common is SON p.Arg1972Cys (c.5914C>T) in the general population?

SON p.Arg1972Cys (c.5914C>T) is very rare (popmax 0.00226%, amr) (gnomAD).

What do computational predictors say about SON p.Arg1972Cys (c.5914C>T)?

AlphaMissense predicts likely pathogenic (score 0.9434) — an in-silico prediction, not a clinical call.

SON p.Arg1972Cys

c.5914C>T · rs1296386775 · VCV1983507

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9434 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00226%, amr)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.9434	likely pathogenic
REVEL	0.302	indeterminate
SaProt	LLR -12.85	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP 4.2, phastCons 1
Regional constraint	o/e 0.62	unconstrained · MANE · 2,181 bp · p 1.3e-08 · regional, not allelic
Overall
CADD	23.4	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

Grpmax group 0.00226% Admixed American · 1/44,218 alleles

Overall 0.000267% 4/1,496,362 alleles · very rare exomes 4/1,346,832 · genomes 0/149,530 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00226%	44,218
Remaining individualsnot grpmax-eligible	0.00174%	57,318
African / African-American	0.00145%	69,194
European (non-Finnish)	8.85e-05%	1,129,334

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: SON
Protein: p.Arg1972Cys
Coding: c.5914C>T
MANE Select: NM_138927
dbSNP: rs1296386775
Type: single nucleotide variant
Location: chr21:33555145 (GRCh38)
Gene constraint: LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 36.48 · 4 PDB
Residue 1972: the 'disordered' region; the '7 x 7 aa repeats of p-s-r-r-s-r-[ts]' region; the '2 x 19 aa repeats of p-s-r-r-r-r-s-r-s-v-v-r-r-r-s-f-s-i-s' region

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

Similar variants

SON p.Arg1972His Uncertain significance ★ ⚠ same residue
SON c.6321+1G>A Pathogenic ★★ same type
SON p.Arg1081Ter Pathogenic ★★ same type
SON p.Arg1112Ter Pathogenic ★★ same type
SON p.Arg1825Ter Pathogenic ★★ same type
SON p.Arg2008Ter Pathogenic ★★ same type
SON p.Gln96Ter Pathogenic/Likely pathogenic ★★ same type
SON c.6657+160A>C 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/son-p-arg1972cys (accessed [today's date]).

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