Is AK2 p.Val19Met (c.55G>A) pathogenic?

AK2 p.Val19Met (c.55G>A) is classified Uncertain significance in AK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-21). AlphaMissense: likely pathogenic (0.8659); Ultra-rare (popmax 0.012%, amr); Associated with reticular dysgenesis.

What condition is associated with AK2 p.Val19Met (c.55G>A)?

AK2 p.Val19Met (c.55G>A) is associated with reticular dysgenesis (ClinVar).

How common is AK2 p.Val19Met (c.55G>A) in the general population?

AK2 p.Val19Met (c.55G>A) is ultra-rare (popmax 0.012%, amr) (gnomAD).

How is Reticular dysgenesis inherited?

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

What do computational predictors say about AK2 p.Val19Met (c.55G>A)?

AlphaMissense predicts likely pathogenic (score 0.8659) — an in-silico prediction, not a clinical call.

AK2 p.Val19Met

c.55G>A · rs761910421 · VCV651057

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8659 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.012%, amr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

reticular dysgenesis

Computational evidence

Protein change
AlphaMissense	0.8659	likely pathogenic
REVEL	0.507	indeterminate
SaProt	LLR -9.35	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 2.8, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 24 kb · p 0.0069 · regional, not allelic
Overall
CADD	23.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.012% Admixed American · 7/58,402 alleles

Filtering AF 0.00557% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00399%

Overall 0.000691% 10/1,447,310 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.012%	8,343
South Asian	0.00113%	88,704
European (non-Finnish)	0.00017%	586,810

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: AK2
Protein: p.Val19Met
Coding: c.55G>A
MANE Select: NM_001625
dbSNP: rs761910421
Type: single nucleotide variant
Location: chr1:33036774 (GRCh38)
Gene constraint: LOEUF 0.954 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.49 · 3 PDB
Residue 19: a β-strand

Full AK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

reticular dysgenesis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Reticular dysgenesis (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

AK2 p.Val19= Likely benign ★ same residue
AK2 c.330+5G>A Pathogenic ★★ same condition
AK2 c.498+1G>A Pathogenic/Likely pathogenic ★★ same condition
AK2 p.Ala182Asp Pathogenic/Likely pathogenic ★★ same condition
AK2 p.Arg103Trp Pathogenic/Likely pathogenic ★★ same condition
AK2 p.Arg175Pro Likely pathogenic ★★ same condition
AK2 p.Met1Val Pathogenic ★★ same condition
AK2 p.Ala212Thr Uncertain significance ★★ ⚠ 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/ak2-p-val19met (accessed [today's date]).

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