Is DNAJA2 p.Arg201Ser (c.601C>A) pathogenic?

DNAJA2 p.Arg201Ser (c.601C>A) is classified Uncertain significance in DNAJA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-02). AlphaMissense: likely pathogenic (0.9461); Absent from gnomAD v4.1.

How common is DNAJA2 p.Arg201Ser (c.601C>A) in the general population?

DNAJA2 p.Arg201Ser (c.601C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNAJA2 p.Arg201Ser (c.601C>A)?

AlphaMissense predicts likely pathogenic (score 0.9461) — an in-silico prediction, not a clinical call.

DNAJA2 p.Arg201Ser

c.601C>A · VCV4013473

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9461 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,414)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9461	likely pathogenic
REVEL	0.518	indeterminate
SaProt	LLR -14.41	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 0.67	unconstrained · MANE · 17 kb · p 8e-14 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,414). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DNAJA2
Protein: p.Arg201Ser
Coding: c.601C>A
MANE Select: NM_005880
Type: single nucleotide variant
Location: chr16:46964784 (GRCh38)
Gene constraint: LOEUF 0.258 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.10 · 1 PDB

Full DNAJA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJA2 p.Gly79Ser Uncertain significance ★★ ⚠ same type
DNAJA2 p.Arg107Gln Uncertain significance ★ ⚠ same type
DNAJA2 p.Arg110Gly Uncertain significance ★ ⚠ same type
DNAJA2 p.Arg112Gly Uncertain significance ★ ⚠ same type
DNAJA2 p.Arg165Gln Uncertain significance ★ ⚠ same type
DNAJA2 p.Arg388His Uncertain significance ★ ⚠ same type
DNAJA2 p.Arg68Lys Uncertain significance ★ ⚠ same type
DNAJA2 p.Arg75Trp 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/dnaja2-p-arg201ser (accessed [today's date]).

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