Is ANKRD11 p.Ser411= (c.1233G>A) pathogenic?

ANKRD11 p.Ser411= (c.1233G>A) is classified Likely benign in ANKRD11 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-06-01). Very rare (popmax 0.00534%, afr); Associated with KBG syndrome.

What condition is associated with ANKRD11 p.Ser411= (c.1233G>A)?

ANKRD11 p.Ser411= (c.1233G>A) is associated with KBG syndrome (ClinVar).

How common is ANKRD11 p.Ser411= (c.1233G>A) in the general population?

ANKRD11 p.Ser411= (c.1233G>A) is very rare (popmax 0.00534%, afr) (gnomAD).

ANKRD11 p.Ser411=

c.1233G>A · rs768010691 · VCV2143164

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00534%, afr)

Conditions

KBG syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.161	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -9.8	GERP -3.2
Overall
CADD	0.191	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00534% African / African-American · 4/74,920 alleles

Filtering AF 0.00267% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00236%

Overall 0.00335% 54/1,613,818 alleles · very rare exomes 44/1,461,666 · genomes 10/152,152 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00534%	18,730
East Asian	0.00445%	22,451
European (non-Finnish)	0.00356%	28,096
Admixed American	0.00333%	30,000
Remaining individualsnot grpmax-eligible	0.0032%	31,241
South Asian	0.0022%	45,539

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.Ser411=
Coding: c.1233G>A
MANE Select: NM_013275
dbSNP: rs768010691
Type: single nucleotide variant
Location: chr16:89285309 (GRCh38)
Gene constraint: LOEUF 0.132 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 39.44
Residue 411: a modified residue (phosphoserine); 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.Ser411Leu Uncertain significance ★★ ⚠ same residue
ANKRD11 p.Ser411Ter Pathogenic ★ 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-ser411 (accessed [today's date]).

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