Is KDM5C p.Pro940fs (c.2813_2816dup) pathogenic?

KDM5C p.Pro940fs (c.28132816dup) is classified Pathogenic in KDM5C (ClinVar, Single submitter, 1 submitter; last evaluated 2020-06-11). Absent from gnomAD; Associated with syndromic X-linked intellectual disability Claes-Jensen type.

What condition is associated with KDM5C p.Pro940fs (c.2813_2816dup)?

KDM5C p.Pro940fs (c.2813_2816dup) is associated with syndromic X-linked intellectual disability Claes-Jensen type (ClinVar).

How common is KDM5C p.Pro940fs (c.2813_2816dup) in the general population?

KDM5C p.Pro940fs (c.2813_2816dup) is absent from gnomAD (gnomAD).

KDM5C p.Pro940fs

c.2813_2816dup · rs2519397716 · VCV1805730

Pathogenic Single submitter

Classification

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

syndromic X-linked intellectual disability Claes-Jensen type

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 19 of 26
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.35	GERP -2.2, phastCons 0.004

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: KDM5C
Protein: p.Pro940fs
Coding: c.2813_2816dup
MANE Select: NM_004187
dbSNP: rs2519397716
Type: Duplication
Location: chrX:53196850 (GRCh38)
Structure: AlphaFold pLDDT 72.50 · 2 PDB

Full KDM5C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

syndromic X-linked intellectual disability Claes-Jensen type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KDM5C c.1746+4_1746+7dup Uncertain significance ★★ same condition
KDM5C c.2517-9_2517-7dup Benign/Likely benign ★★ same condition
KDM5C p.Pro940= Likely benign ★★ same residue
KDM5C p.Arg1082fs Pathogenic ★ same condition
KDM5C p.Arg68fs Pathogenic ★ same condition
KDM5C p.Asn73fs Likely pathogenic ★ same condition
KDM5C p.Asp517fs Likely pathogenic ★ same condition
KDM5C p.Cys1047fs 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/kdm5c-p-pro940fs (accessed [today's date]).

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