Is KIF7 p.Ser98= (c.294A>G) pathogenic?

KIF7 p.Ser98= (c.294A>G) is classified Benign/Likely benign in KIF7 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-26). Low-frequency (popmax 1.51%, afr); Associated with acrocallosal syndrome.

What condition is associated with KIF7 p.Ser98= (c.294A>G)?

KIF7 p.Ser98= (c.294A>G) is associated with acrocallosal syndrome (ClinVar).

How common is KIF7 p.Ser98= (c.294A>G) in the general population?

KIF7 p.Ser98= (c.294A>G) is low-frequency (popmax 1.51%, afr) (gnomAD).

KIF7 p.Ser98=

c.294A>G · rs145049849 · VCV263144

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.51%, afr)

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 -5.8	GERP -5.4
Overall
CADD	1.169	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.51% African / African-American · 1,106/73,070 alleles

Filtering AF 1.44% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.41%

Overall 0.0807% 1,246/1,543,440 alleles · low-frequency exomes 588/1,391,088 · genomes 658/152,352 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.51%	66
Admixed American	0.122%	819
Remaining individualsnot grpmax-eligible	0.0803%	1,245
Middle Eastern	0.0502%	1,991
European (non-Finnish)	0.00237%	42,238

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.Ser98=
Coding: c.294A>G
MANE Select: NM_198525
dbSNP: rs145049849
Type: single nucleotide variant
Location: chr15:89652637 (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 98: the kinesin motor domain; a binding site

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 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
KIF7 c.3518-1G>C Likely pathogenic ★★ same condition
KIF7 c.923+2T>G Likely pathogenic ★★ same condition
KIF7 p.Arg1111Ter 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-ser98 (accessed [today's date]).

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