Is ASMT p.Asp122= (c.366C>T) pathogenic?

ASMT p.Asp122= (c.366C>T) is classified Likely benign in ASMT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-03-30). Ultra-rare (popmax 0.0933%, afr); Associated with ASMT-related disorder.

What condition is associated with ASMT p.Asp122= (c.366C>T)?

ASMT p.Asp122= (c.366C>T) is associated with ASMT-related disorder (ClinVar).

How common is ASMT p.Asp122= (c.366C>T) in the general population?

ASMT p.Asp122= (c.366C>T) is ultra-rare (popmax 0.0933%, afr) (gnomAD).

ASMT p.Asp122=

c.366C>T · rs151095769 · VCV3029851

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0933%, afr)

Conditions

ASMT-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.65	GERP -3.6
Overall
CADD	1.329	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0933% African / African-American · 70/74,988 alleles

Filtering AF 0.0757% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0693%

Overall 0.0149% 241/1,613,262 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0933%	1,071
Middle Eastern	0.0535%	1,871
Remaining individualsnot grpmax-eligible	0.0224%	4,460
Admixed American	0.0133%	7,500
European (non-Finnish)	0.0117%	8,549
East Asian	0.00669%	14,957
South Asian	0.00549%	18,207

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.Asp122=
Coding: c.366C>T
MANE Select: NM_001171038
dbSNP: rs151095769
Type: single nucleotide variant
Location: chrX:1624390 (GRCh38)
Structure: AlphaFold pLDDT 95.55 · 2 PDB
Residue 122: 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.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-asp122 (accessed [today's date]).

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