Is ANKRD13D p.Glu264Lys (c.790G>A) pathogenic?

ANKRD13D p.Glu264Lys (c.790G>A) is classified Uncertain significance in ANKRD13D (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-08). AlphaMissense: likely benign (0.197); Very rare (popmax 0.00937%, afr).

How common is ANKRD13D p.Glu264Lys (c.790G>A) in the general population?

ANKRD13D p.Glu264Lys (c.790G>A) is very rare (popmax 0.00937%, afr) (gnomAD).

What do computational predictors say about ANKRD13D p.Glu264Lys (c.790G>A)?

AlphaMissense predicts likely benign (score 0.197) — an in-silico prediction, not a clinical call.

ANKRD13D p.Glu264Lys

c.790G>A · rs371435656 · VCV3123241

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.197 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00937%, afr)

Computational evidence

Protein change
AlphaMissense	0.197	likely benign
REVEL	0.399	indeterminate
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.27 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.6	GERP 1.9, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 13 kb · p 0.00076 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM E177K vs ClinVar E264K) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00937% African / African-American · 7/74,730 alleles

Filtering AF 0.00438% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00309%

Overall 0.000744% 12/1,612,746 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00937%	10,676
South Asian	0.0033%	30,341
Remaining individualsnot grpmax-eligible	0.0016%	62,430
European (non-Finnish)	8.48e-05%	1,179,359

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.Glu264Lys
Coding: c.790G>A
MANE Select: NM_207354
dbSNP: rs371435656
Type: single nucleotide variant
Location: chr11:67299116 (GRCh38)
Gene constraint: LOEUF 0.552 · pLI 0.55 (gnomAD)
Structure: AlphaFold pLDDT 73.38 · 1 PDB

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

Similar variants

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
ANKRD13D p.Arg146Cys 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-glu264lys (accessed [today's date]).

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