Is ANKRD13D p.Arg596Gln (c.1787G>A) pathogenic?

ANKRD13D p.Arg596Gln (c.1787G>A) is classified Uncertain significance in ANKRD13D (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-04). AlphaMissense: likely benign (0.0931); Very rare (popmax 0.00478%, eas).

How common is ANKRD13D p.Arg596Gln (c.1787G>A) in the general population?

ANKRD13D p.Arg596Gln (c.1787G>A) is very rare (popmax 0.00478%, eas) (gnomAD).

What do computational predictors say about ANKRD13D p.Arg596Gln (c.1787G>A)?

AlphaMissense predicts likely benign (score 0.0931) — an in-silico prediction, not a clinical call.

ANKRD13D p.Arg596Gln

c.1787G>A · rs1383544863 · VCV3123194

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0931 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00478%, eas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0931	likely benign
REVEL	0.093	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 2.7, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 13 kb · p 0.00076 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R509Q vs ClinVar R596Q) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00478% East Asian · 2/41,836 alleles

Filtering AF 0.000792% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000488%

Overall 0.00103% 16/1,551,716 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00478%	20,918
African / African-American	0.00136%	73,630
European (non-Finnish)	0.00113%	88,137

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: ANKRD13D
Protein: p.Arg596Gln
Coding: c.1787G>A
MANE Select: NM_207354
dbSNP: rs1383544863
Type: single nucleotide variant
Location: chr11:67302301 (GRCh38)
Gene constraint: LOEUF 0.552 · pLI 0.55 (gnomAD)
Structure: AlphaFold pLDDT 73.38 · 1 PDB
Residue 596: an α-helix; the uim 4 domain; the 'disordered' region

Full ANKRD13D gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANKRD13D p.Arg596Trp Uncertain significance ★ ⚠ same residue
ANKRD13D p.Ala118Val Uncertain significance ★ ⚠ same type
ANKRD13D p.Ala223Val Uncertain significance ★ ⚠ same type
ANKRD13D p.Ala315Gly Uncertain significance ★ ⚠ same type
ANKRD13D p.Ala441Val Uncertain significance ★ ⚠ same type
ANKRD13D p.Ala498Gly Uncertain significance ★ same type
ANKRD13D p.Ala536Thr Uncertain significance ★ ⚠ same type
ANKRD13D p.Arg116His 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/ankrd13d-p-arg596gln (accessed [today's date]).

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