Is KIF1B p.Val993= (c.2979G>A) pathogenic?

KIF1B p.Val993= (c.2979G>A) is classified Likely benign in KIF1B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-17). Very rare (popmax 0.00161%, nfe).

How common is KIF1B p.Val993= (c.2979G>A) in the general population?

KIF1B p.Val993= (c.2979G>A) is very rare (popmax 0.00161%, nfe) (gnomAD).

KIF1B p.Val993=

c.2979G>A · rs1432401534 · VCV1796723

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00161%, nfe)

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 3.3	GERP -0.13, phastCons 1
Overall
CADD	9.132	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00161% European (non-Finnish) · 19/1,179,960 alleles

Filtering AF 0.00103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00083%

Overall 0.00118% 19/1,614,094 alleles · very rare exomes 19/1,461,762 · genomes 0/152,332 · joint denominator

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: KIF1B
Protein: p.Val993=
Coding: c.2979G>A
MANE Select: NM_001365951
dbSNP: rs1432401534
Type: single nucleotide variant
Location: chr1:10334574 (GRCh38)
Gene constraint: LOEUF 0.376 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 66.64 · 1 PDB

Full KIF1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

KIF1B p.Val993Ala Uncertain significance ★ same residue
KIF1B p.Val993Leu Uncertain significance ★ ⚠ same residue
KIF1B c.1434+5G>A Uncertain significance ★★ same type
KIF1B c.1590+5G>A Uncertain significance ★★ same type
KIF1B c.1671-3C>A Uncertain significance ★★ same type
KIF1B c.1671-3C>G Uncertain significance ★★ same type
KIF1B c.1861+3G>A Uncertain significance ★★ same type
KIF1B c.2115+6205C>T Uncertain significance ★★ same type

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/kif1b-p-val993 (accessed [today's date]).

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