Is KIF7 p.Arg780= (c.2338C>A) pathogenic?

KIF7 p.Arg780= (c.2338C>A) is classified Likely benign in KIF7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-27). No allele count reported in gnomAD v4.1 (AN 1,610,196); Associated with acrocallosal syndrome.

What condition is associated with KIF7 p.Arg780= (c.2338C>A)?

KIF7 p.Arg780= (c.2338C>A) is associated with acrocallosal syndrome (ClinVar).

How common is KIF7 p.Arg780= (c.2338C>A) in the general population?

KIF7 p.Arg780= (c.2338C>A) is no allele count reported in gnomAD v4.1 (AN 1,610,196) (gnomAD).

KIF7 p.Arg780=

c.2338C>A · VCV4759925

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,196)

Conditions

acrocallosal 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 4.1	GERP -0.65, phastCons 1
Overall
CADD	8.681	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,610,196). 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: KIF7
Protein: p.Arg780=
Coding: c.2338C>A
MANE Select: NM_198525
Type: single nucleotide variant
Location: chr15:89642259 (GRCh38)
Gene constraint: LOEUF 1.038 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 68.07 · 5 PDB
Residue 780: the 'interaction with smo' region

Full KIF7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

KIF7 p.Arg780Gln Uncertain significance ★ ⚠ same residue
KIF7 p.Arg780Leu Uncertain significance ★ ⚠ same residue
KIF7 p.Arg780Trp Uncertain significance ★ ⚠ same residue
KIF7 c.1443+2T>C Likely pathogenic ★★ same condition
KIF7 c.1561-1G>A Likely pathogenic ★★ same condition
KIF7 c.1789-2A>G Likely pathogenic ★★ same condition
KIF7 c.2593-3C>G Pathogenic ★★ same condition
KIF7 c.328+2T>G 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/kif7-p-arg780 (accessed [today's date]).

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