Is AHNAK2 p.Arg418Ser (c.1254G>T) pathogenic?

AHNAK2 p.Arg418Ser (c.1254G>T) is classified Likely benign in AHNAK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-01). AlphaMissense: likely benign (0.2967); Rare (popmax 0.96%, sas).

How common is AHNAK2 p.Arg418Ser (c.1254G>T) in the general population?

AHNAK2 p.Arg418Ser (c.1254G>T) is rare (popmax 0.96%, sas) (gnomAD).

What do computational predictors say about AHNAK2 p.Arg418Ser (c.1254G>T)?

AlphaMissense predicts likely benign (score 0.2967) — an in-silico prediction, not a clinical call.

AHNAK2 p.Arg418Ser

c.1254G>T · rs41307096 · VCV2644891

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2967 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.96%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Computational evidence

Protein change
AlphaMissense	0.2967	likely benign
REVEL	0.134	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.1	GERP -2.9
Regional constraint	o/e 1.23	unconstrained · MANE · 32 kb · p 4.7e-50 · regional, not allelic
Overall
CADD	1.895	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.96% South Asian · 874/91,058 alleles

Filtering AF 0.907% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.886%

Overall 0.648% 10,435/1,610,150 alleles · rare exomes 9,760/1,457,900 · genomes 675/152,250 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.96%	104
European (non-Finnish)	0.73%	137
Remaining individualsnot grpmax-eligible	0.604%	166
Admixed American	0.487%	206
Middle Eastern	0.363%	275
Finnishnot grpmax-eligible	0.203%	492
Ashkenazi Jewishnot grpmax-eligible	0.145%	688
African / African-American	0.116%	862

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: AHNAK2
Protein: p.Arg418Ser
Coding: c.1254G>T
MANE Select: NM_138420
dbSNP: rs41307096
Type: single nucleotide variant
Location: chr14:104954197 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)

Full AHNAK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AHNAK2 p.Glu3598Lys Uncertain significance ★★ ⚠ same type
AHNAK2 p.Gly4376Ser Uncertain significance ★★ ⚠ same type
AHNAK2 p.Lys2479Arg Uncertain significance ★★ ⚠ same type
AHNAK2 p.Lys3309Asn Uncertain significance ★★ ⚠ same type
AHNAK2 p.Val1351Met Uncertain significance ★★ ⚠ same type
AHNAK2 p.Ala1115Val Benign/Likely benign ★★ same type
AHNAK2 p.Ala1323Thr Likely benign ★★ same type
AHNAK2 p.Ala1818Thr Benign/Likely benign ★★ 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/ahnak2-p-arg418ser (accessed [today's date]).

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