Is KIF14 p.Asn537Ser (c.1610A>G) pathogenic?

KIF14 p.Asn537Ser (c.1610A>G) is classified Uncertain significance in KIF14 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-25). AlphaMissense: likely benign (0.2285); Very rare (popmax 0.00711%, afr); Associated with Inborn genetic diseases.

What condition is associated with KIF14 p.Asn537Ser (c.1610A>G)?

KIF14 p.Asn537Ser (c.1610A>G) is associated with Inborn genetic diseases (ClinVar).

How common is KIF14 p.Asn537Ser (c.1610A>G) in the general population?

KIF14 p.Asn537Ser (c.1610A>G) is very rare (popmax 0.00711%, afr) (gnomAD).

What do computational predictors say about KIF14 p.Asn537Ser (c.1610A>G)?

AlphaMissense predicts likely benign (score 0.2285) — an in-silico prediction, not a clinical call.

KIF14 p.Asn537Ser

c.1610A>G · VCV3863917

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2285 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00711%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2285	likely benign
REVEL	0.364	indeterminate
SaProt	LLR -7.88	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 65 kb · p 0.00011 · regional, not allelic
Overall
CADD	22.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00711% African / African-American · 5/70,362 alleles

Filtering AF 0.00278% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00181%

Overall 0.000524% 8/1,527,304 alleles · very rare exomes 3/1,375,158 · genomes 5/152,146 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00711%	14,072
Admixed American	0.0021%	47,518
South Asian	0.00126%	79,268
European (non-Finnish)	8.82e-05%	1,133,156

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: KIF14
Protein: p.Asn537Ser
Coding: c.1610A>G
MANE Select: NM_014875
Type: single nucleotide variant
Location: chr1:200605892 (GRCh38)
Gene constraint: LOEUF 0.65 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.68
Residue 537: the kinesin motor domain; a UniProt-annotated variant site (in mcph20; drastically decreased expression at the mrna level; loss of localization at the midbody during cytokinesis and consequently loss of cit/crik recruitment to the midbody); the 'required for microtubule-binding with high affinity' region

Full KIF14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KIF14 p.Arg1624His Uncertain significance ★★ ⚠ same condition
KIF14 p.Arg609His Uncertain significance ★★ ⚠ same condition
KIF14 p.Arg699Cys Uncertain significance ★★ ⚠ same condition
KIF14 p.Asn153Ser Uncertain significance ★★ ⚠ same condition
KIF14 p.Asp193Gly Uncertain significance ★★ ⚠ same condition
KIF14 p.Asp504Glu Uncertain significance ★★ ⚠ same condition
KIF14 p.Gln1288Lys Uncertain significance ★★ ⚠ same condition
KIF14 p.Gln1376Glu Uncertain significance ★★ ⚠ 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/kif14-p-asn537ser (accessed [today's date]).

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