Is AMN p.Leu279= (c.835C>T) pathogenic?

AMN p.Leu279= (c.835C>T) is classified Likely benign in AMN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-27). Rare (popmax 0.183%, afr); Associated with Imerslund-Grasbeck syndrome.

What condition is associated with AMN p.Leu279= (c.835C>T)?

AMN p.Leu279= (c.835C>T) is associated with Imerslund-Grasbeck syndrome, Imerslund-Grasbeck syndrome type 2 (ClinVar).

How common is AMN p.Leu279= (c.835C>T) in the general population?

AMN p.Leu279= (c.835C>T) is rare (popmax 0.183%, afr) (gnomAD).

How is Imerslund-Gräsbeck syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

AMN p.Leu279=

c.835C>T · rs371426960 · VCV697343

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.183%, afr)

Conditions

Imerslund-Grasbeck syndrome

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 -0.25	GERP -1.3, phastCons 0.002
Overall
CADD	6.73	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.183% African / African-American · 134/73,206 alleles

Filtering AF 0.158% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.148%

Overall 0.00922% 143/1,550,496 alleles · rare exomes 67/1,398,212 · genomes 76/152,284 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.183%	546
Admixed American	0.00586%	17,053
South Asian	0.00357%	28,023
Remaining individualsnot grpmax-eligible	0.00167%	60,050
European (non-Finnish)	0.000174%	573,691

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: AMN
Protein: p.Leu279=
Coding: c.835C>T
MANE Select: NM_030943
dbSNP: rs371426960
Type: single nucleotide variant
Location: chr14:102929729 (GRCh38)
Gene constraint: LOEUF 1.446 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 80.78 · 1 PDB

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

Disease context

Imerslund-Grasbeck syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Imerslund-Grasbeck syndrome type 2

For Imerslund-Gräsbeck syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Finland)

Similar variants

AMN p.Leu279Met Uncertain significance ★ ⚠ same residue
AMN c.208-1G>C Pathogenic/Likely pathogenic ★★ same condition
AMN c.296-1G>A Likely pathogenic ★★ same condition
AMN c.44-1G>A Likely pathogenic ★★ same condition
AMN c.760+1G>A Likely pathogenic ★★ same condition
AMN c.844-1G>C Likely pathogenic ★★ same condition
AMN p.Thr41Ile Likely pathogenic ★★ ⚠ same condition
AMN p.Trp391Ter Pathogenic/Likely pathogenic ★★ 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/amn-p-leu279 (accessed [today's date]).

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