Is ANKRD11 p.Pro2028= (c.6084C>T) pathogenic?

ANKRD11 p.Pro2028= (c.6084C>T) is classified Benign in ANKRD11 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-05-11). Common (popmax 5.73%, afr) — too common for a highly-penetrant pathogenic allele; Associated with Inborn genetic diseases.

What condition is associated with ANKRD11 p.Pro2028= (c.6084C>T)?

ANKRD11 p.Pro2028= (c.6084C>T) is associated with Inborn genetic diseases, KBG syndrome (ClinVar).

ANKRD11 p.Pro2028=

Q: How common is ANKRD11 p.Pro2028= (c.6084C>T) in the general population?

ANKRD11 p.Pro2028= (c.6084C>T) is common (popmax 5.73%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.6084C>T · rs189297725 · VCV585416

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 5.73%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -20	GERP -3.1
Overall
CADD	0.059	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.73% African / African-American · 4,262/74,406 alleles

Filtering AF 5.58% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.53%

Overall 0.294% 4,682/1,594,300 alleles · common exomes 2,242/1,441,950 · genomes 2,440/152,350 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.73%	17
Remaining individualsnot grpmax-eligible	0.316%	316
Admixed American	0.292%	342
Middle Eastern	0.0352%	2,844
South Asian	0.00668%	14,980
European (non-Finnish)	0.00411%	24,356

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: ANKRD11
Protein: p.Pro2028=
Coding: c.6084C>T
MANE Select: NM_013275
dbSNP: rs189297725
Type: single nucleotide variant
Location: chr16:89280458 (GRCh38)
Gene constraint: LOEUF 0.132 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 39.44

Full ANKRD11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: KBG syndrome

Similar variants

ANKRD11 p.Pro2028Arg Uncertain significance ★ ⚠ same residue
ANKRD11 p.Pro2028Leu Uncertain significance ★ ⚠ same residue
ANKRD11 c.744+1G>T Pathogenic ★★ same condition
ANKRD11 c.745-2A>G Likely pathogenic ★★ same condition
ANKRD11 c.7470+1G>C Pathogenic ★★ same condition
ANKRD11 c.7569+1G>A Pathogenic ★★ same condition
ANKRD11 c.7569+1G>C Likely pathogenic ★★ same condition
ANKRD11 c.7570-1G>A Pathogenic ★★ 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/ankrd11-p-pro2028 (accessed [today's date]).

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