Is KIF5C p.Phe320= (c.960C>T) pathogenic?

KIF5C p.Phe320= (c.960C>T) is classified Likely benign in KIF5C (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-04). Ultra-rare (popmax 0.0823%, mid); Associated with KIF5C-related disorder.

What condition is associated with KIF5C p.Phe320= (c.960C>T)?

KIF5C p.Phe320= (c.960C>T) is associated with KIF5C-related disorder (ClinVar).

How common is KIF5C p.Phe320= (c.960C>T) in the general population?

KIF5C p.Phe320= (c.960C>T) is ultra-rare (popmax 0.0823%, mid) (gnomAD).

KIF5C p.Phe320=

c.960C>T · rs764512878 · VCV3052973

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0823%, mid)

Conditions

KIF5C-related disorder

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 0.9	GERP -3.3, phastCons 1
Overall
CADD	11.99	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0823% Middle Eastern · 5/6,072 alleles

Filtering AF 0.0324% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.021%

Overall 0.00403% 65/1,613,234 alleles · ultra-rare exomes 56/1,461,088 · genomes 9/152,146 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0823%	1,214
Remaining individualsnot grpmax-eligible	0.00801%	12,488
Admixed American	0.005%	19,987
African / African-American	0.00401%	24,964
European (non-Finnish)	0.00398%	25,098
South Asian	0.0022%	45,443

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: KIF5C
Protein: p.Phe320=
Coding: c.960C>T
MANE Select: NM_004522
dbSNP: rs764512878
Type: single nucleotide variant
Location: chr2:148950454 (GRCh38)
Gene constraint: LOEUF 0.249 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 78.70
Residue 320: the kinesin motor domain

Full KIF5C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

KIF5C-related disorder

Similar variants

KIF5C p.Ala194Thr Uncertain significance ★ ⚠ same condition
KIF5C p.Thr691Met Uncertain significance ★ ⚠ same condition
KIF5C p.Glu658Lys Uncertain significance ⚠ same condition
KIF5C p.Gly826Ala Uncertain significance ⚠ same condition
KIF5C p.His954Pro Uncertain significance ⚠ same condition
KIF5C c.*5A>C Likely benign same condition
KIF5C p.Ala84= Likely benign same condition
KIF5C p.Asn358= Likely benign 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/kif5c-p-phe320 (accessed [today's date]).

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