Is ASMT p.Asp287= (c.861C>T) pathogenic?

ASMT p.Asp287= (c.861C>T) is classified Benign in ASMT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-02-16). Common (popmax 28.3%, eas) — too common for a highly-penetrant pathogenic allele; Associated with ASMT-related disorder.

What condition is associated with ASMT p.Asp287= (c.861C>T)?

ASMT p.Asp287= (c.861C>T) is associated with ASMT-related disorder (ClinVar).

ASMT p.Asp287=

Q: How common is ASMT p.Asp287= (c.861C>T) in the general population?

ASMT p.Asp287= (c.861C>T) is common (popmax 28.3%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.861C>T · rs4933063 · VCV3036285

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 28.3%, eas) — too common for a highly-penetrant pathogenic allele

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 -7.6	GERP -3.9
Overall
CADD	0.006	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 28.3% East Asian · 12,705/44,856 alleles

Filtering AF 27.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 27.7%

Overall 9.28% 149,772/1,613,588 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	28.3%	4
Admixed American	13.6%	7
African / African-American	12.7%	8
Finnishnot grpmax-eligible	10.4%	10
Remaining individualsnot grpmax-eligible	10.3%	10
European (non-Finnish)	8.28%	12
Ashkenazi Jewishnot grpmax-eligible	6.92%	14
Middle Eastern	6.77%	15
South Asian	6.69%	15
Amishnot grpmax-eligible	5.26%	19

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.Asp287=
Coding: c.861C>T
MANE Select: NM_001171038
dbSNP: rs4933063
Type: single nucleotide variant
Location: chrX:1636511 (GRCh38)
Structure: AlphaFold pLDDT 95.55 · 2 PDB
Residue 287: an α-helix

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

Disease context

ASMT-related disorder

Similar variants

ASMT p.Arg210= Likely benign same condition
ASMT p.Asp122= Likely 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-asp287 (accessed [today's date]).

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