Is ASMT p.Arg210= (c.630C>G) pathogenic?

ASMT p.Arg210= (c.630C>G) is classified Likely benign in ASMT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-08-10). Ultra-rare (popmax 0.0174%, nfe); Associated with ASMT-related disorder.

What condition is associated with ASMT p.Arg210= (c.630C>G)?

ASMT p.Arg210= (c.630C>G) is associated with ASMT-related disorder (ClinVar).

How common is ASMT p.Arg210= (c.630C>G) in the general population?

ASMT p.Arg210= (c.630C>G) is ultra-rare (popmax 0.0174%, nfe) (gnomAD).

ASMT p.Arg210=

c.630C>G · rs758073107 · VCV3060990

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0174%, nfe)

Conditions

ASMT-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.24	GERP 0.14, phastCons 0.001
Overall
CADD	0.716	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0174% European (non-Finnish) · 33/189,848 alleles

Filtering AF 0.0127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0111%

Overall 0.0108% 39/359,972 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0174%	5,753
Remaining individualsnot grpmax-eligible	0.0148%	6,767
African / African-American	0.00823%	12,154

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: ASMT
Protein: p.Arg210=
Coding: c.630C>G
MANE Select: NM_001171038
dbSNP: rs758073107
Type: single nucleotide variant
Location: chrX:1632771 (GRCh38)
Structure: AlphaFold pLDDT 95.55 · 2 PDB
Residue 210: a UniProt-annotated variant site (nearly abolishes enzyme activity); a binding site; a β-strand

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

Disease context

ASMT-related disorder

Similar variants

ASMT p.Asp122= Likely benign same condition
ASMT p.Asp287= Benign same condition
ASMT p.Trp190Arg Benign same condition
ASMT c.910+8del Likely benign same condition
ASMT p.Lys81Glu Likely benign ★★ same type
ASMT c.562+2T>C Conflicting classifications of pathogenicity ★ same type
ASMT p.Asn17Lys Uncertain significance ★ same type
ASMT p.Cys29Ter 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/asmt-p-arg210 (accessed [today's date]).

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