Is KIF11 p.Ser992fs (c.2972dup) pathogenic?

KIF11 p.Ser992fs (c.2972dup) is classified Likely pathogenic in KIF11 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-01). Absent from gnomAD; Associated with microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability.

How common is KIF11 p.Ser992fs (c.2972dup) in the general population?

KIF11 p.Ser992fs (c.2972dup) is absent from gnomAD (gnomAD).

KIF11 p.Ser992fs

Q: What condition is associated with KIF11 p.Ser992fs (c.2972dup)?

KIF11 p.Ser992fs (c.2972dup) is associated with microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (ClinVar).

c.2972dup · rs1554863246 · VCV495254

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability

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 21 of 22
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.3	GERP -3.9

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: KIF11
Protein: p.Ser992fs
Coding: c.2972dup
MANE Select: NM_004523
dbSNP: rs1554863246
Type: Duplication
Location: chr10:92650449 (GRCh38)
Gene constraint: LOEUF 0.184 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 74.46 · 62 PDB

Full KIF11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KIF11 p.Ala373fs Pathogenic ★ same condition
KIF11 p.Asn684Ter Pathogenic ★ same condition
KIF11 p.Asp975fs Likely pathogenic ★ same condition
KIF11 p.His354fs Likely pathogenic ★ same condition
KIF11 p.Leu293delinsLysLeuGluIleTer Likely pathogenic ★ same condition
KIF11 p.Thr126fs Likely pathogenic ★ same condition
KIF11 c.2161-1G>A Pathogenic/Likely pathogenic ★★ same condition
KIF11 c.2548-1G>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/kif11-p-ser992fs (accessed [today's date]).

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