Is PITPNM3 p.Arg900Ser (c.2697_2698delinsAA) pathogenic?

PITPNM3 p.Arg900Ser (c.26972698delinsAA) is classified Uncertain significance in PITPNM3 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-11-23). No gnomAD frequency available for this variant.

How common is PITPNM3 p.Arg900Ser (c.2697_2698delinsAA) in the general population?

PITPNM3 p.Arg900Ser (c.2697_2698delinsAA) is no gnomAD frequency available for this variant (gnomAD).

PITPNM3 p.Arg900Ser

c.2697_2698delinsAA · rs1914054912 · VCV845979

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.5	GERP 0.84, phastCons 1
Regional constraint	o/e 1.17	unconstrained · MANE · 2,325 bp · p 0.026 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PITPNM3
Protein: p.Arg900Ser
Coding: c.2697_2698delinsAA
MANE Select: NM_031220
dbSNP: rs1914054912
Type: Indel
Location: chr17:6455565 (GRCh38)
Gene constraint: LOEUF 0.354 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 66.73 · 1 PDB

Full PITPNM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PITPNM3 p.Arg900= Conflicting classifications of pathogenicity ★ same residue
PITPNM3 p.Arg900Cys Uncertain significance ★ same residue
PITPNM3 p.Gln931Pro Uncertain significance ★★ same type
PITPNM3 c.1773+18_1773+19delinsAT Uncertain significance ★ same type
PITPNM3 p.Ala80Met Uncertain significance ★ same type
PITPNM3 p.Asp810Asn Uncertain significance ★ same type
PITPNM3 p.Gly13Cys Uncertain significance ★ same type
PITPNM3 p.Met534Asn 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/pitpnm3-p-arg900ser (accessed [today's date]).

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