Is ANKRD11 p.Lys1237fs (c.3708_3709del) pathogenic?

ANKRD11 p.Lys1237fs (c.37083709del) is classified Pathogenic/Likely pathogenic in ANKRD11 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-12-28). Absent from gnomAD; Associated with ANKRD11-related disorder.

What condition is associated with ANKRD11 p.Lys1237fs (c.3708_3709del)?

ANKRD11 p.Lys1237fs (c.3708_3709del) is associated with ANKRD11-related disorder, KBG syndrome (ClinVar).

How common is ANKRD11 p.Lys1237fs (c.3708_3709del) in the general population?

ANKRD11 p.Lys1237fs (c.3708_3709del) is absent from gnomAD (gnomAD).

ANKRD11 p.Lys1237fs

c.3708_3709del · rs1567572265 · VCV565310

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ANKRD11-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 9 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.93	GERP 0.93, phastCons 0.82

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ANKRD11
Protein: p.Lys1237fs
Coding: c.3708_3709del
MANE Select: NM_013275
dbSNP: rs1567572265
Type: Deletion
Location: chr16:89282833 (GRCh38)
Gene constraint: LOEUF 0.132 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 39.44
Residue 1237: the 'disordered' region

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

Disease context

ANKRD11-related disorder

Also linked: KBG syndrome

Similar variants

ANKRD11 p.Ala2265fs Pathogenic ★★ same condition
ANKRD11 p.Ala2323fs Pathogenic ★★ same condition
ANKRD11 p.Arg1466fs Pathogenic ★★ same condition
ANKRD11 p.Arg1497fs Pathogenic ★★ same condition
ANKRD11 p.Arg1832fs Pathogenic/Likely pathogenic ★★ same condition
ANKRD11 p.Arg493fs Pathogenic ★★ same condition
ANKRD11 p.Asn452fs Pathogenic/Likely pathogenic ★★ same condition
ANKRD11 p.Asp1104fs Pathogenic/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-lys1237fs (accessed [today's date]).

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