Is ANKRD11 p.Pro2007= (c.6021C>T) pathogenic?

ANKRD11 p.Pro2007= (c.6021C>T) is classified Likely benign in ANKRD11 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-10-17). Very rare (popmax 0.00401%, afr); Associated with KBG syndrome.

What condition is associated with ANKRD11 p.Pro2007= (c.6021C>T)?

ANKRD11 p.Pro2007= (c.6021C>T) is associated with KBG syndrome (ClinVar).

How common is ANKRD11 p.Pro2007= (c.6021C>T) in the general population?

ANKRD11 p.Pro2007= (c.6021C>T) is very rare (popmax 0.00401%, afr) (gnomAD).

ANKRD11 p.Pro2007=

c.6021C>T · rs976983352 · VCV1082875

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00401%, afr)

Conditions

KBG syndrome

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 -0.027	GERP -3.1, phastCons 0.66
Overall
CADD	0.628	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00401% African / African-American · 3/74,898 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.000372% 6/1,611,206 alleles · very rare exomes 4/1,458,984 · genomes 2/152,222 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00401%	24,966
Admixed American	0.00334%	29,957
European (non-Finnish)	8.48e-05%	1,179,302

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.Pro2007=
Coding: c.6021C>T
MANE Select: NM_013275
dbSNP: rs976983352
Type: single nucleotide variant
Location: chr16:89280521 (GRCh38)
Gene constraint: LOEUF 0.132 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 39.44
Residue 2007: the 'disordered' region

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

Disease context

KBG syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ANKRD11 p.Pro2007Leu Benign/Likely benign ★★ 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
ANKRD11 c.892+1G>A Likely 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-pro2007 (accessed [today's date]).

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