Is KIF7 p.Arg960= (c.2880C>G) pathogenic?

KIF7 p.Arg960= (c.2880C>G) is classified Likely benign in KIF7 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-17). Ultra-rare (popmax 0.0221%, sas); Associated with acrocallosal syndrome.

What condition is associated with KIF7 p.Arg960= (c.2880C>G)?

KIF7 p.Arg960= (c.2880C>G) is associated with acrocallosal syndrome (ClinVar).

How common is KIF7 p.Arg960= (c.2880C>G) in the general population?

KIF7 p.Arg960= (c.2880C>G) is ultra-rare (popmax 0.0221%, sas) (gnomAD).

KIF7 p.Arg960=

c.2880C>G · rs761354914 · VCV1648591

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0221%, sas)

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 0.18	GERP -5.4, phastCons 0.89
Overall
CADD	6.279	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0221% South Asian · 20/90,578 alleles

Filtering AF 0.0146% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0122%

Overall 0.00131% 21/1,606,498 alleles · ultra-rare exomes 20/1,454,404 · genomes 1/152,094 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0221%	4,529
Remaining individualsnot grpmax-eligible	0.0016%	62,368

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: KIF7
Protein: p.Arg960=
Coding: c.2880C>G
MANE Select: NM_198525
dbSNP: rs761354914
Type: single nucleotide variant
Location: chr15:89632835 (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 960: 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.Arg960Cys Uncertain significance ★★ ⚠ same residue
KIF7 p.Arg960Gly Uncertain significance ★ ⚠ same residue
KIF7 p.Arg960His 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-arg960 (accessed [today's date]).

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